7TAV | pdb_00007tav

Crystal Structure of the PBP2_YvgL_like protein Lmo1041 from Listeria monocytogene

PDB DOI: https://doi.org/10.2210/pdb7TAV/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Listeria monocytogenes
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-12-21 Released: 2021-12-29
Deposition Author(s): Kim, Y., Maltseva, N., Grimshaw, S., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free:
0.251 (Depositor), 0.251 (DCC)
R-Value Work:
0.213 (Depositor), 0.212 (DCC)
R-Value Observed:
0.215 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 7TAV

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of the PBP2_YvgL_like protein Lmo1041 from Listeria monocytogenes

Kim, Y., Maltseva, N., Grimshaw, S., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 153.75 kDa
Atom Count: 10,464
Modeled Residue Count: 1,351
Deposited Residue Count: 1,398
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Molybdate ABC transporter substrate-binding protein	A, B, C, D, E A, B, C, D, E, F	233	Listeria monocytogenes	Mutation(s): 0 Gene Names: modA
UniProt
Find proteins for A0A5D5LL32 (Listeria monocytogenes) Explore A0A5D5LL32 Go to UniProtKB: A0A5D5LL32
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A5D5LL32
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain GA [auth F] SDF format, chain L [auth A] SDF format, chain N [auth B] SDF format, chain T [auth C] SDF format, chain W [auth D] MOL2 format, chain BA [auth E] MOL2 format, chain GA [auth F] MOL2 format, chain L [auth A] MOL2 format, chain N [auth B] MOL2 format, chain T [auth C] MOL2 format, chain W [auth D] mmCIF format, chain BA [auth E] mmCIF format, chain GA [auth F] mmCIF format, chain L [auth A] mmCIF format, chain N [auth B] mmCIF format, chain T [auth C] mmCIF format, chain W [auth D]	BA [auth E] GA [auth F] L [auth A] N [auth B] T [auth C] BA [auth E], GA [auth F], L [auth A], N [auth B], T [auth C], W [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth E] Focus chain GA [auth F] Focus chain L [auth A] Focus chain N [auth B] Focus chain T [auth C] Focus chain W [auth D] Interactions & Density Focus chain BA [auth E] Focus chain GA [auth F] Focus chain L [auth A] Focus chain N [auth B] Focus chain T [auth C] Focus chain W [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain CA [auth F] SDF format, chain G [auth A] MOL2 format, chain CA [auth F] MOL2 format, chain G [auth A] mmCIF format, chain CA [auth F] mmCIF format, chain G [auth A]	CA [auth F], G [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CA [auth F] Focus chain G [auth A] Interactions & Density Focus chain CA [auth F] Focus chain G [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain DA [auth F] SDF format, chain EA [auth F] SDF format, chain FA [auth F] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain M [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain U [auth D] SDF format, chain V [auth D] SDF format, chain X [auth E] SDF format, chain Y [auth E] SDF format, chain Z [auth E] MOL2 format, chain AA [auth E] MOL2 format, chain DA [auth F] MOL2 format, chain EA [auth F] MOL2 format, chain FA [auth F] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] MOL2 format, chain X [auth E] MOL2 format, chain Y [auth E] MOL2 format, chain Z [auth E] mmCIF format, chain AA [auth E] mmCIF format, chain DA [auth F] mmCIF format, chain EA [auth F] mmCIF format, chain FA [auth F] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain M [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D] mmCIF format, chain X [auth E] mmCIF format, chain Y [auth E] mmCIF format, chain Z [auth E]	AA [auth E] DA [auth F] EA [auth F] FA [auth F] H [auth A] AA [auth E], DA [auth F], EA [auth F], FA [auth F], H [auth A], I [auth A], J [auth A], K [auth A], M [auth B], P [auth C], Q [auth C], R [auth C], S [auth C], U [auth D], V [auth D], X [auth E], Y [auth E], Z [auth E]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain X [auth E] Focus chain Y [auth E] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth E] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain X [auth E] Focus chain Y [auth E] Focus chain Z [auth E]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain O [auth B] MOL2 format, chain O [auth B] mmCIF format, chain O [auth B]	O [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain O [auth B] Interactions & Density Focus chain O [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.251 (Depositor), 0.251 (DCC)
R-Value Work: 0.213 (Depositor), 0.212 (DCC)
R-Value Observed: 0.215 (Depositor)

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.715	α = 90
b = 113.715	β = 90
c = 114.598	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MOLREP	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-12-29

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History (Full details and data files)

Version 1.0: 2021-12-29
Type: Initial release
Version 1.1: 2022-01-05
Changes: Structure summary
Version 1.2: 2023-04-19
Changes: Database references, Structure summary
Version 1.3: 2024-04-03
Changes: Data collection, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.