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- PDB-7s91: Structure of the malate racemase mar2 apoprotein from Thermoanaer... -

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Basic information

Entry
Database: PDB / ID: 7s91
TitleStructure of the malate racemase mar2 apoprotein from Thermoanaerobacterium thermosaccharolyticum at 2.25 angstroms resolution
ComponentsMalate racemase Mar2
KeywordsISOMERASE / Catalytic activity / isomerase activity / racemase and epimerase activity racemase acting on hydroxy acids and derivatives
Function / homology: / : / Lactate racemase C-terminal domain / LarA-like, C-terminal domain / lactate racemase activity / LarA-like, N-terminal / : / Lactate racemase N-terminal domain / Uncharacterized protein
Function and homology information
Biological speciesThermoanaerobacterium thermosaccharolyticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsGatreddi, S. / Hausinger, R.P. / Hu, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE 1807073 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM128959 United States
CitationJournal: Biometals / Year: 2023
Title: Structural and mutational characterization of a malate racemase from the LarA superfamily.
Authors: Gatreddi, S. / Urdiain-Arraiza, J. / Desguin, B. / Hausinger, R.P. / Hu, J.
History
DepositionSep 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Malate racemase Mar2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6303
Polymers47,5591
Non-polymers712
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.460, 100.450, 132.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-502-

CL

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Components

#1: Protein Malate racemase Mar2 / Nickel-dependent lactate racemase


Mass: 47559.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacterium thermosaccharolyticum (strain ATCC 7956 / DSM 571 / NCIB 9385 / NCA 3814) (bacteria)
Strain: ATCC 7956 / DSM 571 / NCIB 9385 / NCA 3814 / Gene: Tthe_2432 / Production host: Lactococcus lactis (lactic acid bacteria) / Strain (production host): NZ3900 / References: UniProt: D9TSN9
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.41 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100 mM HEPES (pH 8.0), 200 mM NaCl, 30% PEG 3350. The crystal was cryo protected in a solution containing 100 mM HEPES (pH 8.0), 200 mM NaCl, and 35% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Sep 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.25→29.38 Å / Num. obs: 23233 / % possible obs: 99.9 % / Redundancy: 4 % / CC1/2: 0.994 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.063 / Rrim(I) all: 0.131 / Net I/σ(I): 7.3
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.844 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3344 / CC1/2: 0.549 / Rpim(I) all: 0.475 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18.2-3874-000refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6D6Z

6d6z


Resolution: 2.25→29.38 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2395 1185 5.1 %
Rwork0.2057 --
obs0.2076 23226 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→29.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3050 0 2 88 3140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083107
X-RAY DIFFRACTIONf_angle_d1.0354206
X-RAY DIFFRACTIONf_dihedral_angle_d13.772431
X-RAY DIFFRACTIONf_chiral_restr0.058479
X-RAY DIFFRACTIONf_plane_restr0.006543
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.350.31231220.27972731X-RAY DIFFRACTION100
2.35-2.480.28491670.25722690X-RAY DIFFRACTION100
2.48-2.630.28511410.24482739X-RAY DIFFRACTION100
2.63-2.830.25041480.23752722X-RAY DIFFRACTION100
2.83-3.120.33581400.22882755X-RAY DIFFRACTION100
3.12-3.570.2481390.2082755X-RAY DIFFRACTION100
3.57-4.50.20691660.1752771X-RAY DIFFRACTION100
4.5-29.380.20081620.17982878X-RAY DIFFRACTION99

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