6HHS | pdb_00006hhs

MamM CTD E289D - Cadmium form

PDB DOI: https://doi.org/10.2210/pdb6HHS/pdb

Classification: METAL TRANSPORT
Organism(s): Magnetospirillum gryphiswaldense, Magnetospirillum gryphiswaldense MSR-1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2018-08-29 Released: 2019-09-18
Deposition Author(s): Barber-Zucker, S., Zarivach, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.290 (Depositor), 0.297 (DCC)
R-Value Work:
0.250 (Depositor), 0.252 (DCC)
R-Value Observed:
0.252 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

MamM CTD E289D - Cadmium form

Barber-Zucker, S., Zarivach, R.

To be published.

Macromolecule Content

Total Structure Weight: 86.5 kDa
Atom Count: 4,710
Modeled Residue Count: 587
Deposited Residue Count: 764
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Magnetosome protein MamM, Cation efflux protein family	A, B, C, D, E A, B, C, D, E, F, G	108	Magnetospirillum gryphiswaldense	Mutation(s): 1 Gene Names: mamM, mgI491, MGR_4095
UniProt
Find proteins for V6F235 (Magnetospirillum gryphiswaldense (strain DSM 6361 / JCM 21280 / NBRC 15271 / MSR-1)) Explore V6F235 Go to UniProtKB: V6F235
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	V6F235
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable C-terminal region of MamM CTD E289D - Cadmium form	H [auth M]	8	Magnetospirillum gryphiswaldense MSR-1	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CD (Subject of Investigation/LOI) Query on CD Download:Ideal Coordinates CCD File SDF format, chain CA [auth E] SDF format, chain DA [auth E] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain Q [auth B] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain Z [auth D] MOL2 format, chain CA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain CA [auth E] mmCIF format, chain DA [auth E] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain Z [auth D]	CA [auth E] DA [auth E] I [auth A] J [auth A] K [auth A] CA [auth E], DA [auth E], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], Q [auth B], T [auth C], U [auth C], V [auth C], Z [auth D]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain CA [auth E] Focus chain DA [auth E] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain Q [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain Z [auth D] Interactions & Density Focus chain CA [auth E] Focus chain DA [auth E] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain Q [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain Z [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain EA [auth E] SDF format, chain FA [auth F] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain R [auth B] SDF format, chain W [auth C] SDF format, chain X [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain EA [auth E] MOL2 format, chain FA [auth F] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain R [auth B] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain EA [auth E] mmCIF format, chain FA [auth F] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain R [auth B] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C]	AA [auth D] BA [auth D] EA [auth E] FA [auth F] N [auth A] AA [auth D], BA [auth D], EA [auth E], FA [auth F], N [auth A], O [auth A], R [auth B], W [auth C], X [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain EA [auth E] Focus chain FA [auth F] Focus chain N [auth A] Focus chain O [auth A] Focus chain R [auth B] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain EA [auth E] Focus chain FA [auth F] Focus chain N [auth A] Focus chain O [auth A] Focus chain R [auth B] Focus chain W [auth C] Focus chain X [auth C]
BME Query on BME Download:Ideal Coordinates CCD File SDF format, chain GA [auth F] SDF format, chain P [auth A] SDF format, chain S [auth B] SDF format, chain Y [auth C] MOL2 format, chain GA [auth F] MOL2 format, chain P [auth A] MOL2 format, chain S [auth B] MOL2 format, chain Y [auth C] mmCIF format, chain GA [auth F] mmCIF format, chain P [auth A] mmCIF format, chain S [auth B] mmCIF format, chain Y [auth C]	GA [auth F], P [auth A], S [auth B], Y [auth C]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain GA [auth F] Focus chain P [auth A] Focus chain S [auth B] Focus chain Y [auth C] Interactions & Density Focus chain GA [auth F] Focus chain P [auth A] Focus chain S [auth B] Focus chain Y [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.290 (Depositor), 0.297 (DCC)
R-Value Work: 0.250 (Depositor), 0.252 (DCC)
R-Value Observed: 0.252 (Depositor)

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.599	α = 90
b = 94.545	β = 91.76
c = 107.49	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
STARANISO	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-09-18

Deposition Author(s):

Barber-Zucker, S.

Zarivach, R.

Funding Organization	Location	Grant Number
	Israel	Israel Science Foundation 167/16
	Israel	Israel Ministry of Science, Technology and Space

Revision History (Full details and data files)

Version 1.0: 2019-09-18
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description