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- PDB-3isv: Crystal structure of glutamate racemase from Listeria monocytogen... -

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Basic information

Entry
Database: PDB / ID: 3isv
TitleCrystal structure of glutamate racemase from Listeria monocytogenes in complex with acetate ion
ComponentsGlutamate racemase
KeywordsISOMERASE / glutamate racemase / structural genomics / Cell wall biogenesis/degradation / Peptidoglycan synthesis / Center for Structural Genomics of Infectious Diseases / CSGID / Cell shape
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 1 / Aspartate and glutamate racemases signature 1. / 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 ...Glutamate racemase / Asp/Glu racemase, active site 1 / Aspartate and glutamate racemases signature 1. / 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
ACETATE ION / Glutamate racemase
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMajorek, K.A. / Chruszcz, M. / Skarina, T. / Onopriyenko, O. / Stam, J. / Anderson, W.F. / Savchenko, A. / Bujnicki, J.M. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal structure of glutamate racemase from Listeria monocytogenes in complex with acetate ion
Authors: Majorek, K.A. / Chruszcz, M. / Skarina, T. / Onopriyenko, O. / Stam, J. / Anderson, W.F. / Savchenko, A. / Bujnicki, J.M. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionAug 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8608
Polymers59,5912
Non-polymers2696
Water7,620423
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Glutamate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0647
Polymers29,7951
Non-polymers2696
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Glutamate racemase


Theoretical massNumber of molelcules
Total (without water)29,7951
Polymers29,7951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.763, 66.763, 258.602
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-294-

HOH

Detailsdimer

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Components

#1: Protein Glutamate racemase /


Mass: 29795.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: EGD-E / Gene: lmo1237, murI, racE / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 star magic / References: UniProt: Q8Y7N7, glutamate racemase
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 423 / 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: 2.42 Å3/Da / Density % sol: 49.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG8K 18%, CaAcetate 0.2M, NaCacod 0.1m, pH 6.5, 10mM L-Glutamic acid, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 14, 2009 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 51135 / Num. obs: 51135 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 23.3
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 4 % / Rmerge(I) obs: 0.621 / Mean I/σ(I) obs: 2 / Rsym value: 0.621 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-3000MOLREPphasing
REFMAC5.5.0062refinement
Cootmodel building
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3hfr

3hfr


Resolution: 1.85→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.938 / SU B: 6.507 / SU ML: 0.089 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22394 2591 5.1 %RANDOM
Rwork0.17186 ---
obs0.17444 48365 99.46 %-
all-48365 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.287 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20 Å20 Å2
2--0.66 Å20 Å2
3----1.31 Å2
Refinement stepCycle: LAST / Resolution: 1.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4029 0 12 423 4464
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224207
X-RAY DIFFRACTIONr_bond_other_d0.0060.022788
X-RAY DIFFRACTIONr_angle_refined_deg1.6291.9765724
X-RAY DIFFRACTIONr_angle_other_deg0.97736878
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7345552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.69324.487156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.26815737
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2021520
X-RAY DIFFRACTIONr_chiral_restr0.0990.2682
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214688
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02792
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.961.52709
X-RAY DIFFRACTIONr_mcbond_other0.2711.51101
X-RAY DIFFRACTIONr_mcangle_it1.73124392
X-RAY DIFFRACTIONr_scbond_it3.231498
X-RAY DIFFRACTIONr_scangle_it5.0114.51331
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 196 -
Rwork0.25 3475 -
obs--99.81 %
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)
11.38760.81610.12841.6410.081.4828-0.12340.1783-0.1751-0.12890.1685-0.1342-0.03180.1471-0.04510.1231-0.10640.01420.1956-0.01940.04327.737-15.342-6.449
21.25190.4390.37431.0853-0.17851.9167-0.05140.06330.1146-0.02950.11570.14310.0055-0.1946-0.06420.1173-0.07180.00130.15950.03070.07459.079-15.0034.222
31.88510.60260.46920.88310.34622.445-0.16490.18740.0928-0.17190.16780.0082-0.26960.0992-0.0030.1837-0.124-0.00750.16330.03790.048326.771-5.372-9.033
42.08570.58610.68361.84290.55122.5399-0.04110.0884-0.0567-0.03170.1142-0.1587-0.23180.2104-0.07310.1665-0.0071-0.00530.14730.00580.017337.362-6.85626.685
50.6216-0.18070.48871.2431-0.70352.6492-0.1215-0.02160.00510.08190.16170.011-0.3941-0.0714-0.04020.1432-0.0055-0.00050.1201-0.00250.015928.641.61822.635
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 91
2X-RAY DIFFRACTION2A92 - 205
3X-RAY DIFFRACTION3A206 - 265
4X-RAY DIFFRACTION4B1 - 81
5X-RAY DIFFRACTION5B82 - 266

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