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- PDB-3uho: Crystal Structure of Glutamate Racemase from Campylobacter jejuni... -

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Basic information

Entry
Database: PDB / ID: 3uho
TitleCrystal Structure of Glutamate Racemase from Campylobacter jejuni subsp. jejuni
ComponentsGlutamate racemase
KeywordsISOMERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / alpha-beta sandwich fold
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
D-GLUTAMIC ACID / Glutamate racemase
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMaltseva, N. / Mulligan, R. / Kwon, K. / Kim, Y. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of Glutamate Racemase from Campylobacter jejuni subsp. jejuni
Authors: Maltseva, N. / Mulligan, R. / Kwon, K. / Kim, Y. / Anderson, W.F. / Joachimiak, A. / CSGID
History
DepositionNov 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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 / _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.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,51814
Polymers61,7272
Non-polymers79112
Water2,666148
1
A: Glutamate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2106
Polymers30,8631
Non-polymers3475
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glutamate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3088
Polymers30,8631
Non-polymers4447
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.308, 74.384, 50.144
Angle α, β, γ (deg.)90.00, 96.53, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-265-

HOH

21A-288-

HOH

31B-310-

HOH

41B-324-

HOH

Detailstwo monomers in the asymmetric unit

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glutamate racemase


Mass: 30863.424 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Strain: NCTC 11168 / Gene: Cj1652c, murI / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q9PM24, glutamate racemase

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Non-polymers , 5 types, 160 molecules

#2: Chemical ChemComp-DGL / D-GLUTAMIC ACID


Type: D-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CA / CALCIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.17 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2M Calcium Chloride, 0.1M Tris pH8.0, 16% PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 21, 2011 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 25698 / Num. obs: 25698 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 34.13 Å2 / Rsym value: 0.109 / Net I/σ(I): 7.9
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 1273 / Rsym value: 0.503 / % possible all: 97.7

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIX(phenix.refine: dev_851)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3UHF

3uhf


Resolution: 2.2→34.601 Å / SU ML: 0.6 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1294 5.07 %random
Rwork0.19 ---
all0.193 25515 --
obs0.193 25515 98.37 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.607 Å2 / ksol: 0.325 e/Å3
Displacement parametersBiso mean: 42.7 Å2
Baniso -1Baniso -2Baniso -3
1--3.1442 Å2-0 Å21.1906 Å2
2---6.374 Å20 Å2
3---9.5182 Å2
Refinement stepCycle: LAST / Resolution: 2.2→34.601 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3962 0 45 148 4155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054298
X-RAY DIFFRACTIONf_angle_d0.8735816
X-RAY DIFFRACTIONf_dihedral_angle_d14.561601
X-RAY DIFFRACTIONf_chiral_restr0.062655
X-RAY DIFFRACTIONf_plane_restr0.003742
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.2001-2.28820.30441280.23982665279398
2.2882-2.39230.27471470.22392686283398
2.3923-2.51840.30171510.21572640279198
2.5184-2.67610.25051390.20772668280798
2.6761-2.88260.28971190.20872718283799
2.8826-3.17250.24171470.20272705285299
3.1725-3.63120.20961760.1852666284299
3.6312-4.57320.1841400.15872721286199
4.5732-34.6050.24481470.18362752289998
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)
17.50263.00651.21738.61610.38015.42610.12220.18530.83180.2547-0.1388-0.1122-0.2912-0.0406-0.00920.22590.02130.01340.18390.06270.254-19.75278.110213.3378
23.76910.5949-0.71322.2203-0.5542.6307-0.23041.13060.202-0.57880.22940.0065-0.0192-0.197-0.00040.30510.0204-0.00490.40770.03390.1862-26.2570.92566.6269
33.0189-0.48261.87591.7332-0.38485.60260.12660.637-0.0124-0.2143-0.0461-0.2429-0.13340.3977-0.06470.2596-0.00490.05790.2695-0.01440.2655-15.3005-2.922610.3132
45.8495-2.1715-0.35883.38650.18031.1395-0.0932-0.3882-0.26820.01530.06920.1230.055-0.13850.0280.1382-0.0091-0.0220.10810.02230.1545-22.8365-7.602127.818
57.49951.882-2.35634.3766-2.65037.9595-0.1615-0.17860.25810.16530.1588-0.11310.18760.2485-0.01670.16210.0087-0.06240.1449-0.05070.2015-15.96930.835927.0152
68.15240.89192.49124.30651.08344.5369-0.27070.11861.09190.06960.24390.1389-0.4070.35940.08180.48140.04580.03650.25660.08640.4749-21.722515.126413.1315
77.64133.488-1.50748.1377-1.36676.7697-0.20090.2967-0.5434-0.3072-0.17630.45890.0553-0.06080.34090.22640.0435-0.01830.1798-0.05770.3174-55.1275-12.662212.7827
85.96894.58221.09337.56912.27643.103-0.39510.57060.0247-0.32850.30920.38090.13050.14360.0840.21620.0597-0.03740.20520.01730.1713-50.1208-8.946310.0744
94.9871.99410.97796.29970.31324.3057-0.08120.82160.3053-0.83030.02070.2822-0.01750.22610.07220.3350.044-0.03240.3940.12670.2547-52.5315-1.67334.3628
103.3925-1.1186-4.06473.2283.84287.94060.07960.5005-0.1131-0.5079-0.37170.4361-0.88-0.69880.27550.2630.0655-0.08530.24370.01480.309-63.6894-0.985414.2007
117.6429-3.2461-0.00242.20430.71520.6281-0.045-0.13960.389-0.07070.04640.1006-0.10070.0602-0.01010.2214-0.02120.0080.12040.01220.2804-54.50674.084825.1618
128.2707-1.55660.09781.6732-1.13223.5837-0.1336-0.9993-0.03920.24160.07080.1732-0.02210.10640.03720.2454-0.01260.03310.22060.0220.266-50.5902-1.767533.1849
135.64522.77560.91559.07746.51398.67520.01030.46590.17680.3143-0.24110.40970.3238-0.54880.24690.1736-0.00750.03790.1865-0.01690.2916-64.7153-6.266720.0134
145.79631.4867-2.92614.94320.05164.1959-0.0830.8148-0.3763-0.12910.15230.91460.2116-0.4898-0.03340.43020.0385-0.05670.2989-0.02120.5431-58.4085-18.21428.8954
158.21872.0552-3.93726.9315-1.23227.4739-0.2567-0.568-1.17480.3659-0.0108-0.29260.05380.03260.20060.46310.0610.00310.22230.01420.4378-48.3212-21.939916.7332
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:22)
2X-RAY DIFFRACTION2chain 'A' and (resseq 23:60)
3X-RAY DIFFRACTION3chain 'A' and (resseq 61:104)
4X-RAY DIFFRACTION4chain 'A' and (resseq 105:182)
5X-RAY DIFFRACTION5chain 'A' and (resseq 183:214)
6X-RAY DIFFRACTION6chain 'A' and (resseq 215:250)
7X-RAY DIFFRACTION7chain 'B' and (resseq 1:21)
8X-RAY DIFFRACTION8chain 'B' and (resseq 22:43)
9X-RAY DIFFRACTION9chain 'B' and (resseq 44:84)
10X-RAY DIFFRACTION10chain 'B' and (resseq 85:104)
11X-RAY DIFFRACTION11chain 'B' and (resseq 105:156)
12X-RAY DIFFRACTION12chain 'B' and (resseq 157:198)
13X-RAY DIFFRACTION13chain 'B' and (resseq 199:214)
14X-RAY DIFFRACTION14chain 'B' and (resseq 215:233)
15X-RAY DIFFRACTION15chain 'B' and (resseq 234:250)

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