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- PDB-1tm0: Crystal Structure of the putative proline racemase from Brucella ... -

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Basic information

Entry
Database: PDB / ID: 1tm0
TitleCrystal Structure of the putative proline racemase from Brucella melitensis, Northeast Structural Genomics Target LR31
ComponentsPROLINE RACEMASE
KeywordsISOMERASE / STRUCTURAL GENOMICS / alpha-beta protein that resembles double-beta barrel / in each of which an alpha helix is sandwiched / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology4-hydroxyproline epimerase / 4-hydroxyproline epimerase activity / Proline racemase family / Proline racemase / Diaminopimelate Epimerase; Chain A, domain 1 / Diaminopimelate Epimerase; Chain A, domain 1 / Roll / Alpha Beta / Protein BMEI1586
Function and homology information
Biological speciesBrucella melitensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsForouhar, F. / Chen, Y. / Xiao, R. / Ho, C.K. / Ma, L.-C. / Cooper, B. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J.STRUCT.FUNCT.GENOM. / Year: 2007
Title: Functional insights from structural genomics.
Authors: Forouhar, F. / Kuzin, A. / Seetharaman, J. / Lee, I. / Zhou, W. / Abashidze, M. / Chen, Y. / Yong, W. / Janjua, H. / Fang, Y. / Wang, D. / Cunningham, K. / Xiao, R. / Acton, T.B. / ...Authors: Forouhar, F. / Kuzin, A. / Seetharaman, J. / Lee, I. / Zhou, W. / Abashidze, M. / Chen, Y. / Yong, W. / Janjua, H. / Fang, Y. / Wang, D. / Cunningham, K. / Xiao, R. / Acton, T.B. / Pichersky, E. / Klessig, D.F. / Porter, C.W. / Montelione, G.T. / Tong, L.
History
DepositionJun 10, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROLINE RACEMASE
B: PROLINE RACEMASE


Theoretical massNumber of molelcules
Total (without water)77,1192
Polymers77,1192
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: PROLINE RACEMASE
B: PROLINE RACEMASE

A: PROLINE RACEMASE
B: PROLINE RACEMASE


Theoretical massNumber of molelcules
Total (without water)154,2384
Polymers154,2384
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area9220 Å2
ΔGint-50 kcal/mol
Surface area46710 Å2
MethodPISA
3
A: PROLINE RACEMASE


Theoretical massNumber of molelcules
Total (without water)38,5591
Polymers38,5591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
B: PROLINE RACEMASE


Theoretical massNumber of molelcules
Total (without water)38,5591
Polymers38,5591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)138.027, 77.363, 77.416
Angle α, β, γ (deg.)90.00, 124.11, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PROLINE RACEMASE


Mass: 38559.449 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis (bacteria) / Strain: 16M / Plasmid: pET21(BL21) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q8YFD6, proline racemase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Mutation: protein has C-tag (LEHHHHHH) / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.25 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG 3350, pH 7, 200mM potassium thiocyanate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97904 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 4, 2004 / Details: Mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97904 Å / Relative weight: 1
ReflectionResolution: 2.8→28.57 Å / Num. all: 29250 / Num. obs: 26270 / % possible obs: 84.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 9.3 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.076 / Net I/σ(I): 13.5
Reflection shellResolution: 2.8→2.98 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.181 / Mean I/σ(I) obs: 5.1 / Num. unique all: 2887 / Rsym value: 0.182 / % possible all: 98.2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
SOLVEphasing
RESOLVEmodel building
CNSrefinement
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→28.57 Å / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure.
RfactorNum. reflection% reflectionSelection details
Rfree0.312 2482 -random
Rwork0.236 ---
all0.312 29250 --
obs0.236 26270 84.3 %-
Displacement parametersBiso mean: 33.5 Å2
Baniso -1Baniso -2Baniso -3
1--10.59 Å20 Å22.93 Å2
2---1.32 Å20 Å2
3---11.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.8→28.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4684 0 0 34 4718
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.2
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_improper_angle_d0.9
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.028
RfactorNum. reflection% reflection
Rfree0.373 182 -
Rwork0.294 --
obs-1683 9.8 %

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