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- PDB-2vd9: The crystal structure of alanine racemase from Bacillus anthracis... -

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Basic information

Entry
Database: PDB / ID: 2vd9
TitleThe crystal structure of alanine racemase from Bacillus anthracis (BA0252) with bound L-Ala-P
ComponentsALANINE RACEMASE
KeywordsISOMERASE / PYRIDOXAL 5'-PHOSPHATE / PEPTIDOGLYCAN SYNTHESIS / PLP / OPPF / L-ALANINE / D-ALANINE / PYRIDOXAL PHOSPHATE / STRUCTURAL GENOMICS / ALANINE RACEMASE / SPORE GERMINATION / OXFORD PROTEIN PRODUCTION FACILITY (OPPF) / STRUCTURAL PROTEOMICS IN EUROPE (SPINE)
Function / homology
Function and homology information


alanine racemase / D-alanine biosynthetic process / alanine racemase activity / peptidoglycan biosynthetic process / pyridoxal phosphate binding / metal ion binding / cytosol
Similarity search - Function
Alanine racemase, pyridoxal-phosphate attachment site / Alanine racemase pyridoxal-phosphate attachment site. / Alanine racemase / Alanine racemase, C-terminal / Alanine racemase, C-terminal domain / Alanine racemase, C-terminal domain / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Alanine racemase, N-terminal / Alanine racemase, N-terminal domain / Lyase, Ornithine Decarboxylase; Chain A, domain 1 ...Alanine racemase, pyridoxal-phosphate attachment site / Alanine racemase pyridoxal-phosphate attachment site. / Alanine racemase / Alanine racemase, C-terminal / Alanine racemase, C-terminal domain / Alanine racemase, C-terminal domain / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Alanine racemase, N-terminal / Alanine racemase, N-terminal domain / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Alanine racemase / Alanine racemase/group IV decarboxylase, C-terminal / PLP-binding barrel / TIM Barrel / Alpha-Beta Barrel / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-EPC / Chem-IN5 / Alanine racemase / Alanine racemase
Similarity search - Component
Biological speciesBACILLUS ANTHRACIS (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAu, K. / Ren, J. / Walter, T.S. / Harlos, K. / Nettleship, J.E. / Owens, R.J. / Stuart, D.I. / Esnouf, R.M. / Oxford Protein Production Facility (OPPF) / Structural Proteomics in Europe (SPINE)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Structures of an Alanine Racemase from Bacillus Anthracis (Ba0252) in the Presence and Absence of (R)-1-Aminoethylphosphonic Acid (L-Ala-P).
Authors: Au, K. / Ren, J. / Walter, T.S. / Harlos, K. / Nettleship, J.E. / Owens, R.J. / Stuart, D.I. / Esnouf, R.M.
History
DepositionOct 1, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2008Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2012Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB", "BB" IN EACH CHAIN ON SHEET RECORDS ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB", "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALANINE RACEMASE
B: ALANINE RACEMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,30212
Polymers88,7022
Non-polymers1,60010
Water15,691871
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10510 Å2
ΔGint-36 kcal/mol
Surface area27590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.692, 96.504, 140.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A4 - 394
2112B4 - 394

NCS oper: (Code: given
Matrix: (-0.99662, 0.0821, 6.0E-5), (0.08207, 0.9963, 0.02569), (0.00205, 0.02561, -0.99967)
Vector: -13.372, 1.461, -71.057)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ALANINE RACEMASE


Mass: 44350.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: ALL LYSINES DIMETHYLATED EXCEPT K41 AND K260 / Source: (gene. exp.) BACILLUS ANTHRACIS (anthrax bacterium) / Strain: AMES / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): ROSETTA PLYSS
References: UniProt: Q81VF6, UniProt: A0A6L7HC45*PLUS, alanine racemase

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Non-polymers , 5 types, 881 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-IN5 / {1-[(3-HYDROXY-METHYL-5-PHOSPHONOOXY-METHYL-PYRIDIN-4-YLMETHYL)-AMINO]-ETHYL}-PHOSPHONIC ACID


Mass: 356.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H18N2O8P2
#5: Chemical ChemComp-EPC / (1S)-1-[((1E)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYLENE)AMINO]ETHYLPHOSPHONIC ACID


Mass: 354.190 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O8P2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 871 / 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: 2.28 Å3/Da / Density % sol: 46 % / Description: NONE
Crystal growpH: 6.5
Details: 25% (W/V) POLYETHYLENE GLYCOL 3350, 0.1M BIS-TRIS PH6.5, SOAKED IN 10MM L-ALA-P FOR 45 MINUTES, CRYOPROTECTED IN 25% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.979
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 20, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 48124 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.23 / Net I/σ(I): 7.1
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 1.2 / % possible all: 9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VD8

2vd8


Resolution: 2.1→45.64 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.913 / SU B: 5.555 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.261 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.239 2434 5.1 %RANDOM
Rwork0.188 ---
obs0.19 45596 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.1→45.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6196 0 94 871 7161
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0226431
X-RAY DIFFRACTIONr_bond_other_d0.0020.024237
X-RAY DIFFRACTIONr_angle_refined_deg1.1952.0018767
X-RAY DIFFRACTIONr_angle_other_deg0.9123.00110276
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2885770
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.06423.546282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.56915895
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7711540
X-RAY DIFFRACTIONr_chiral_restr0.0680.2980
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027134
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021326
X-RAY DIFFRACTIONr_nbd_refined0.1890.21289
X-RAY DIFFRACTIONr_nbd_other0.1950.24970
X-RAY DIFFRACTIONr_nbtor_refined0.1750.23106
X-RAY DIFFRACTIONr_nbtor_other0.0840.23177
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2636
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2310.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1930.231
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.76924970
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.91436230
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.53523039
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.85932537
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
2264tight positional0.030.05
2929medium positional0.410.5
2264tight thermal0.392
2929medium thermal0.585
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.324 172
Rwork0.261 3188

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