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- PDB-3out: Crystal structure of glutamate racemase from Francisella tularens... -

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Basic information

Entry
Database: PDB / ID: 3out
TitleCrystal structure of glutamate racemase from Francisella tularensis subsp. tularensis SCHU S4 in complex with D-glutamate.
ComponentsGlutamate racemase
KeywordsISOMERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Glutamate racemase / MurI / Cell envelope / Francisella tularensis subsp. tularensis SCHU S4 / Center for Structural Genomics of Infectious Diseases (CSGID)
Function / homology
Function and homology information


glutamate racemase / glutamate racemase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape
Similarity search - Function
Glutamate racemase / Asp/Glu racemase, active site 2 / Aspartate and glutamate racemases signature 2. / Rossmann fold - #1860 / Asp/Glu racemase / Asp/Glu/hydantoin racemase / Asp/Glu/Hydantoin racemase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
D-GLUTAMIC ACID / Glutamate racemase
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsFilippova, E.V. / Wawrzak, Z. / Onopriyenko, O. / Kudriska, M. / Edwards, A. / Savchenko, A. / Anderson, F.W. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal structure of glutamate racemase from Francisella tularensis subsp. tularensis SCHU S4 in complex with D-glutamate.
Authors: Filippova, E.V. / Wawrzak, Z. / Onopriyenko, O. / Kudriska, M. / Edwards, A. / Savchenko, A. / Anderson, F.W. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionSep 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 27, 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate racemase
B: Glutamate racemase
C: Glutamate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,2616
Polymers89,8193
Non-polymers4413
Water10,827601
1
A: Glutamate racemase
B: Glutamate racemase
C: Glutamate racemase
hetero molecules

A: Glutamate racemase
B: Glutamate racemase
C: Glutamate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,52112
Polymers179,6396
Non-polymers8836
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area15280 Å2
ΔGint-50 kcal/mol
Surface area54980 Å2
MethodPISA
2
A: Glutamate racemase
C: Glutamate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1744
Polymers59,8802
Non-polymers2942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-14 kcal/mol
Surface area20990 Å2
MethodPISA
3
B: Glutamate racemase
hetero molecules

B: Glutamate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1744
Polymers59,8802
Non-polymers2942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area2290 Å2
ΔGint-13 kcal/mol
Surface area21260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.060, 98.060, 154.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Glutamate racemase


Mass: 29939.773 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria)
Gene: FTT_1197c, murI / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q5NFN6, glutamate racemase
#2: Chemical ChemComp-DGL / D-GLUTAMIC ACID


Type: D-peptide linking / Mass: 147.129 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 601 / 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: 2.06 Å3/Da / Density % sol: 40.37 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 25% PEG 3350, 0.1 M Tris, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MAR CCD / Detector: CCD / Date: Aug 13, 2010 / Details: MIRROR
RadiationMonochromator: SI-111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.65→25.2 Å / Num. all: 172747 / Num. obs: 172747 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 12.6 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 14.71
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 11 % / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 3.16 / Num. unique all: 9026 / % possible all: 99.8

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
CCP4model building
MrBUMPphasing
PHENIXmodel building
REFMAC5.5.0109refinement
XSCALEdata scaling
CCP4phasing
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.65→25.22 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.687 / SU ML: 0.058 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1927 4544 5 %RANDOM
Rwork0.16265 ---
obs0.16416 86104 99.87 %-
all-86104 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.396 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å20 Å2
2---0.31 Å20 Å2
3---0.62 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.65→25.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6168 0 30 601 6799
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0226472
X-RAY DIFFRACTIONr_bond_other_d0.0010.024264
X-RAY DIFFRACTIONr_angle_refined_deg1.5371.9798811
X-RAY DIFFRACTIONr_angle_other_deg0.986310572
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8125825
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.6425.394254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.299151162
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1851518
X-RAY DIFFRACTIONr_chiral_restr0.0940.21058
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217141
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021189
X-RAY DIFFRACTIONr_mcbond_it0.9231.54081
X-RAY DIFFRACTIONr_mcbond_other0.2711.51628
X-RAY DIFFRACTIONr_mcangle_it1.6426688
X-RAY DIFFRACTIONr_scbond_it2.90232391
X-RAY DIFFRACTIONr_scangle_it4.4254.52123
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 326 -
Rwork0.232 6295 -
obs--99.73 %

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