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- PDB-2dwu: Crystal Structure of Glutamate Racemase Isoform RacE1 from Bacill... -

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Basic information

Entry
Database: PDB / ID: 2dwu
TitleCrystal Structure of Glutamate Racemase Isoform RacE1 from Bacillus anthracis
ComponentsGlutamate racemase
KeywordsISOMERASE / racemase
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 / Glutamate racemase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMehboob, S. / Santarsiero, B.D. / Johnson, M.E.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structural and Functional Analysis of Two Glutamate Racemase Isozymes from Bacillus anthracis and Implications for Inhibitor Design
Authors: May, M. / Mehboob, S. / Mulhearn, D.C. / Wang, Z. / Yu, H. / Thatcher, G.R.J. / Santarsiero, B.D. / Johnson, M.E. / Mesecar, A.D.
History
DepositionAug 17, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 25, 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_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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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)91,40613
Polymers90,4793
Non-polymers92710
Water21,0241167
1
A: Glutamate racemase
B: Glutamate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9689
Polymers60,3202
Non-polymers6497
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-7 kcal/mol
Surface area21930 Å2
MethodPISA
2
C: Glutamate racemase
hetero molecules

C: Glutamate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8768
Polymers60,3202
Non-polymers5576
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)85.783, 49.659, 198.252
Angle α, β, γ (deg.)90.000, 90.065, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-283-

HOH

21C-283-

HOH

31C-284-

HOH

DetailsA dimer is formed from chain A and B; and a second dimer is formed from chain C and symmetry-related chain C by a two-fold rotation about the b-axis: 1-x, y, -z.

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Components

#1: Protein Glutamate racemase


Mass: 30159.805 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: racE-1 / Plasmid: PET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q81UL8, UniProt: A0A6L8PVU3*PLUS, glutamate racemase
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-DGL / D-GLUTAMIC ACID


Type: D-peptide linking / Mass: 147.129 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H9NO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1167 / 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: 2.33 Å3/Da / Density % sol: 47.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.2
Details: 0.2M potassium fluoride, 20% PEG 3350, 10mM yttrium chloride, pH 9.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 6, 2006 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.53→20 Å / Num. obs: 105445 / % possible obs: 83.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 21.447 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 22.74
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique all% possible all
1.53-1.620.2145.633008844742
1.62-1.740.1688.9663331240565.6
1.74-1.870.117141054081643693
1.87-2.050.08320.21088851602898
2.05-2.290.06326.3994771441998.4
2.29-2.640.05530.4908761299599.1
2.64-3.220.04934.7792261105799.6
3.220.04438.763145874699.8

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å19.83 Å
Translation2.5 Å19.83 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GZM

2gzm


Resolution: 1.6→20 Å / FOM work R set: 0.901 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.194 5039 4.6 %random
Rwork0.162 ---
all-99587 --
obs-99587 90.2 %-
Solvent computationBsol: 59.362 Å2
Displacement parametersBiso mean: 18.684 Å2
Baniso -1Baniso -2Baniso -3
1-0.237 Å20 Å20.046 Å2
2---3.889 Å20 Å2
3---3.652 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6114 0 57 1167 7338
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.506
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
1.6-1.610.27420.20410351077
1.61-1.620.237640.21111251189
1.62-1.630.246670.1911131180
1.63-1.650.22770.19411891266
1.65-1.660.218760.19212821358
1.66-1.670.288640.212601324
1.67-1.680.238920.19113571449
1.68-1.70.206670.17614301497
1.7-1.710.287720.21415451617
1.71-1.720.182810.18315431624
1.72-1.740.207870.18715661653
1.74-1.750.192910.18917871878
1.75-1.770.213830.16418251908
1.77-1.790.2151030.18419132016
1.79-1.80.1971030.17520082111
1.8-1.820.194980.1820622160
1.82-1.840.2241210.1820352156
1.84-1.860.1891180.15519892107
1.86-1.880.221230.17520412164
1.88-1.90.179970.15520592156
1.9-1.920.195880.15920362124
1.92-1.940.1911160.15220212137
1.94-1.960.197940.16621332227
1.96-1.990.1931050.16820502155
1.99-2.020.2151240.17819842108
2.02-2.040.21070.1721052212
2.04-2.070.1871060.16220252131
2.07-2.10.19970.16820672164
2.1-2.140.2111200.16820632183
2.14-2.170.2061160.16720342150
2.17-2.210.1631210.1520762197
2.21-2.250.2121080.16120912199
2.25-2.290.1811090.15120122121
2.29-2.340.1641090.15421272236
2.34-2.390.2041010.15520812182
2.39-2.440.2121110.16620642175
2.44-2.510.1951040.16320722176
2.51-2.570.2341280.1720982226
2.57-2.650.1811290.1520362165
2.65-2.730.2091120.1621642276
2.73-2.830.2061050.16420242129
2.83-2.940.1871140.1621252239
2.94-3.080.1691000.14821582258
3.08-3.240.1871100.15720432153
3.24-3.440.194990.15121762275
3.44-3.710.1931140.14520872201
3.71-4.080.1571090.13121642273
4.08-4.660.1491150.14221062221
4.66-5.850.2091250.1821302255
5.85-200.1961170.20220322149
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4cis.param
X-RAY DIFFRACTION5dgl.paramdgl.top
X-RAY DIFFRACTION6gol.paramgol.top

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