4IYM | pdb_00004iym

Crystal structure of putative methylmalonate-semialdehyde dehydrogenase from Sinorhizobium meliloti 1021 complexed with NAD, target 011934

PDB DOI: https://doi.org/10.2210/pdb4IYM/pdb

Classification: OXIDOREDUCTASE
Organism(s): Sinorhizobium meliloti 1021
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-01-28 Released: 2013-04-03
Deposition Author(s): Malashkevich, V.N., Bhosle, R., Toro, R., Hillerich, B., Gizzi, A., Garforth, S., Kar, A., Chan, M.K., Lafluer, J., Patel, H., Matikainen, B., Chamala, S., Lim, S., Celikgil, A., Villegas, G., Evans, B., Zenchek, W., Love, J., Fiser, A., Khafizov, K., Seidel, R., Bonanno, J.B., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.209 (Depositor), 0.206 (DCC)
R-Value Work:
0.165 (Depositor), 0.164 (DCC)
R-Value Observed:
0.167 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of putative methylmalonate-semialdehyde dehydrogenase from Sinorhizobium meliloti 1021 complexed with NAD, target 011934

Malashkevich, V.N., Bhosle, R., Toro, R., Hillerich, B., Gizzi, A., Garforth, S., Kar, A., Chan, M.K., Lafluer, J., Patel, H., Matikainen, B., Chamala, S., Lim, S., Celikgil, A., Villegas, G., Evans, B., Zenchek, W., Love, J., Fiser, A., Khafizov, K., Seidel, R., Bonanno, J.B., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 926.66 kDa
Atom Count: 64,517
Modeled Residue Count: 7,819
Deposited Residue Count: 8,336
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methylmalonate-semialdehyde dehydrogenase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	521	Sinorhizobium meliloti 1021	Mutation(s): 0 Gene Names: iolA, mmsA, R00726, SMc00781 EC: 1.2.1.27
UniProt
Find proteins for Q92RW4 (Rhizobium meliloti (strain 1021)) Explore Q92RW4 Go to UniProtKB: Q92RW4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q92RW4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain Z [auth G] SDF format, chain X [auth F] SDF format, chain W [auth E] SDF format, chain V [auth D] SDF format, chain U [auth C] SDF format, chain T [auth B] SDF format, chain Q [auth A] SDF format, chain LA [auth P] SDF format, chain JA [auth O] SDF format, chain IA [auth N] SDF format, chain HA [auth M] SDF format, chain GA [auth L] SDF format, chain FA [auth K] SDF format, chain EA [auth J] SDF format, chain CA [auth I] SDF format, chain BA [auth H] MOL2 format, chain Z [auth G] MOL2 format, chain X [auth F] MOL2 format, chain W [auth E] MOL2 format, chain V [auth D] MOL2 format, chain U [auth C] MOL2 format, chain T [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain LA [auth P] MOL2 format, chain JA [auth O] MOL2 format, chain IA [auth N] MOL2 format, chain HA [auth M] MOL2 format, chain GA [auth L] MOL2 format, chain FA [auth K] MOL2 format, chain EA [auth J] MOL2 format, chain CA [auth I] MOL2 format, chain BA [auth H] mmCIF format, chain Z [auth G] mmCIF format, chain X [auth F] mmCIF format, chain W [auth E] mmCIF format, chain V [auth D] mmCIF format, chain U [auth C] mmCIF format, chain T [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain LA [auth P] mmCIF format, chain JA [auth O] mmCIF format, chain IA [auth N] mmCIF format, chain HA [auth M] mmCIF format, chain GA [auth L] mmCIF format, chain FA [auth K] mmCIF format, chain EA [auth J] mmCIF format, chain CA [auth I] mmCIF format, chain BA [auth H]	BA [auth H] CA [auth I] EA [auth J] FA [auth K] GA [auth L] BA [auth H], CA [auth I], EA [auth J], FA [auth K], GA [auth L], HA [auth M], IA [auth N], JA [auth O], LA [auth P], Q [auth A], T [auth B], U [auth C], V [auth D], W [auth E], X [auth F], Z [auth G]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain BA [auth H] Focus chain CA [auth I] Focus chain EA [auth J] Focus chain FA [auth K] Focus chain GA [auth L] Focus chain HA [auth M] Focus chain IA [auth N] Focus chain JA [auth O] Focus chain LA [auth P] Focus chain Q [auth A] Focus chain T [auth B] Focus chain U [auth C] Focus chain V [auth D] Focus chain W [auth E] Focus chain X [auth F] Focus chain Z [auth G] Interactions & Density Focus chain BA [auth H] Focus chain CA [auth I] Focus chain EA [auth J] Focus chain FA [auth K] Focus chain GA [auth L] Focus chain HA [auth M] Focus chain IA [auth N] Focus chain JA [auth O] Focus chain LA [auth P] Focus chain Q [auth A] Focus chain T [auth B] Focus chain U [auth C] Focus chain V [auth D] Focus chain W [auth E] Focus chain X [auth F] Focus chain Z [auth G]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain Y [auth F] SDF format, chain S [auth A] SDF format, chain R [auth A] SDF format, chain KA [auth O] SDF format, chain DA [auth I] SDF format, chain AA [auth G] MOL2 format, chain Y [auth F] MOL2 format, chain S [auth A] MOL2 format, chain R [auth A] MOL2 format, chain KA [auth O] MOL2 format, chain DA [auth I] MOL2 format, chain AA [auth G] mmCIF format, chain Y [auth F] mmCIF format, chain S [auth A] mmCIF format, chain R [auth A] mmCIF format, chain KA [auth O] mmCIF format, chain DA [auth I] mmCIF format, chain AA [auth G]	AA [auth G] DA [auth I] KA [auth O] R [auth A] S [auth A] AA [auth G], DA [auth I], KA [auth O], R [auth A], S [auth A], Y [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth G] Focus chain DA [auth I] Focus chain KA [auth O] Focus chain R [auth A] Focus chain S [auth A] Focus chain Y [auth F] Interactions & Density Focus chain AA [auth G] Focus chain DA [auth I] Focus chain KA [auth O] Focus chain R [auth A] Focus chain S [auth A] Focus chain Y [auth F]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.209 (Depositor), 0.206 (DCC)
R-Value Work: 0.165 (Depositor), 0.164 (DCC)
R-Value Observed: 0.167 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 159.472	α = 90
b = 170.91	β = 106.33
c = 170.466	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-3000	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-04-03

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2013-04-03
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2023-12-06
Changes: Data collection
Version 1.3: 2024-11-06
Changes: Structure summary