There is no agreed standard connector for PC fans, but there is a most choice.

4 Pin Fan

Molex have a special 4 pin fan connector which is designed to accept both 3 pin (no PWM speed control) and 4 pin fans.

Line connector Molex 47054-1000, RS 720-5990
Line connector contacts Molex 47054-1000, RS 172-9178
PCB header Molex 47053-1000, Farnell 2313705

pc_fan_4_pinout

Specification

Intel 4-Wire Pulse Width Modulation (PWM) Controlled Fans​ document.

Tachometer Output Signal

Open-collector or open-drain type output

Motherboard may have to pull up or it may happen to 12V in fan (there is no rule it seems and there will be exceptions to what is considered "normal").

The tachometer output typically comes from a Hall-effect sensor mounted on the motor driver PCB on the fan frame. One or more magnets embedded in the fan rotor hub activate the Hall-effect sensor as they pass by. Fans that typically use an open drain/open collector output.

PWM Control Input Signal

Base frequency is 25kHz with acceptable range from 21kHz to 28kHz.

Input has TTL level and includes pull-up resistor to 5V or to 3.3V in new constructions, but could be pulled up to 12V

Signal is not inverted and 100% PWM means maximal revolutions of fan. Motherboard has open-collector type output.

If left floating fan runs at full speed.

It actually turns out this pin needs a pull up for some fans we've come across, even though the Intel spec document above doesn't specify this (it specifies an open collector output).  The safest solution we've found is to add a pull up resistor to +5V as although some fans are fine with this pin pulled to +12V the Intel spec specifies max 5.25V on this pin.

3 Pin Fan

Can be the same connector with a 3 pin socket plugged into it (pin 4 missing), or a 3 pin version of the header, into which a 4 pin fan can be connected with pin 4 floating causing the fan to run at full speed.

3 pin Molex KK connec​tor:

Line connector Molex 22-01-3037
Line connector contacts Molex 08-50-0114
PCB header Molex 22-23-2031, Farnell 1462950

 

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