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- PDB-6d6z: Structure of the malate racemase apoprotein from Thermoanaerobact... -

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Basic information

Entry
Database: PDB / ID: 6d6z
TitleStructure of the malate racemase apoprotein from Thermoanaerobacterium thermosaccharolyticum
ComponentsMalate racemase Mar2
KeywordsISOMERASE / Lar / lactate racemase
Function / homologyLarA, N-terminal domain / lactate racemase activity / LarA-like, N-terminal / LarA-like, C-terminal domain / Lactate racemase N-terminal domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Lar_N domain-containing protein
Function and homology information
Biological speciesThermoanaerobacterium thermosaccharolyticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.38 Å
AuthorsFellner, M. / Hausinger, R.P. / Hu, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1516126 United States
CitationJournal: Sci Rep / Year: 2020
Title: Uncovering a superfamily of nickel-dependent hydroxyacid racemases and epimerases.
Authors: Desguin, B. / Urdiain-Arraiza, J. / Da Costa, M. / Fellner, M. / Hu, J. / Hausinger, R.P. / Desmet, T. / Hols, P. / Soumillion, P.
History
DepositionApr 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 4, 2020Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.pdbx_description / _struct.title
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Malate racemase Mar2


Theoretical massNumber of molelcules
Total (without water)47,5591
Polymers47,5591
Non-polymers00
Water1,67593
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)72.764, 102.453, 133.953
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-582-

HOH

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Components

#1: Protein Malate racemase Mar2


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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O

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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: 2.62 Å3/Da / Density % sol: 53.14 % / Mosaicity: 0.16 °
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 2 ul ~12 mg/ml LarA (100 mM Tris-HCl pH 7.5, 300 mM NaCl) mixed with 1 ul of reservoir solution. Sitting drop reservoir contained 100 ul of (NH4)2SO4 0.2M, Bis-Tris pH 5.5 0.1M, 25% w/v ...Details: 2 ul ~12 mg/ml LarA (100 mM Tris-HCl pH 7.5, 300 mM NaCl) mixed with 1 ul of reservoir solution. Sitting drop reservoir contained 100 ul of (NH4)2SO4 0.2M, Bis-Tris pH 5.5 0.1M, 25% w/v Polyethylene glycol 3,350. The crystal was soaked for about two minutes in (NH4)2SO4 0.15M, Bis-Tris pH 5.5 0.075M, 32% w/v Polyethylene glycol 3,350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.078 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.078 Å / Relative weight: 1
ReflectionResolution: 2.38→44.41 Å / Num. obs: 20224 / % possible obs: 98.3 % / Redundancy: 9.9 % / Biso Wilson estimate: 42.16 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.042 / Rrim(I) all: 0.132 / Net I/σ(I): 12.3 / Num. measured all: 199614 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.38-2.469.40.99919100.8440.3371.05689.7
8.89-44.418.80.0454470.9990.0150.04799.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.26 Å40.93 Å
Translation5.26 Å40.93 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.6.2data scaling
PHASER2.8.1phasing
PHENIXdev-3092refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HUQ

5huq


Resolution: 2.38→40.933 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 26.48
RfactorNum. reflection% reflection
Rfree0.2386 1951 5.1 %
Rwork0.183 --
obs0.1857 19130 97.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 101.17 Å2 / Biso mean: 50.0573 Å2 / Biso min: 23.93 Å2
Refinement stepCycle: final / Resolution: 2.38→40.933 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2975 0 0 93 3068
Biso mean---44.72 -
Num. residues----393
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3752-2.43460.332960.27562199229582
2.4346-2.50040.341560.276326362792100
2.5004-2.5740.36671300.272726162746100
2.574-2.6570.36931570.24726172774100
2.657-2.7520.26391410.23282596273798
2.752-2.86210.31291540.23232608276298
2.8621-2.99240.28651570.218725962753100
2.9924-3.15010.29921310.21526712802100
3.1501-3.34730.27041290.190626312760100
3.3473-3.60560.26571260.181326432769100
3.6056-3.96820.1851550.154626422797100
3.9682-4.54180.17841300.132326622792100
4.5418-5.71970.18381540.14622570272497
5.7197-40.93860.20811350.16832622275799
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.2051-1.95882.05063.6453-3.0593.79430.21340.2495-0.2534-0.6514-0.03860.32060.6429-0.1017-0.18310.3427-0.035-0.01170.3986-0.0180.3177-17.717-34.1021-49.0015
26.42130.39960.56489.08333.03194.1945-0.13920.05390.3064-0.30880.26560.7678-0.208-0.6103-0.120.23880.002-0.00010.49780.11620.2926-16.4218-37.3033-27.4456
34.7175-4.9593-0.40359.76553.77632.4820.0373-0.21930.05630.6319-0.22910.2437-0.24070.0140.19560.2039-0.002-0.02630.4210.08250.2822-13.2369-31.0448-20.3451
48.77893.8722-4.50544.1955-2.36637.05040.1311-0.44980.15020.3334-0.03530.3055-0.0976-0.181-0.09210.28450.0918-0.0030.24220.01740.252-10.4854-28.6946-21.4514
51.71680.54531.56851.19630.01665.0692-0.0080.19790.1177-0.195-0.0347-0.0916-0.03540.24080.05240.2580.07190.03910.36820.07360.3079-5.4761-30.573-36.5009
62.5867-2.0568-1.48097.28671.21713.46450.2133-0.09660.3757-0.48910.0011-0.8379-0.21710.4493-0.20650.3103-0.02440.04360.41230.00110.3233-14.5835-11.9721-56.4513
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 64 )A2 - 64
2X-RAY DIFFRACTION2chain 'A' and (resid 65 through 91 )A65 - 91
3X-RAY DIFFRACTION3chain 'A' and (resid 92 through 112 )A92 - 112
4X-RAY DIFFRACTION4chain 'A' and (resid 113 through 148 )A113 - 148
5X-RAY DIFFRACTION5chain 'A' and (resid 149 through 268 )A149 - 268
6X-RAY DIFFRACTION6chain 'A' and (resid 269 through 415 )A269 - 415

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