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- PDB-1bd0: ALANINE RACEMASE COMPLEXED WITH ALANINE PHOSPHONATE -

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Basic information

Entry
Database: PDB / ID: 1bd0
TitleALANINE RACEMASE COMPLEXED WITH ALANINE PHOSPHONATE
ComponentsALANINE RACEMASE
KeywordsISOMERASE / ALANINE / PYRIDOXAL PHOSPHATE / ALANINE PHOSPHONATE
Function / homology
Function and homology information


alanine racemase / D-alanine biosynthetic process / alanine racemase activity / peptidoglycan biosynthetic process / pyridoxal phosphate 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-IN5 / Alanine racemase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsStamper, G.F. / Morollo, A.A. / Ringe, D.
Citation
Journal: Biochemistry / Year: 1998
Title: Reaction of alanine racemase with 1-aminoethylphosphonic acid forms a stable external aldimine.
Authors: Stamper, G.F. / Morollo, A.A. / Ringe, D. / Stamper, C.G.
#1: Journal: Biochemistry / Year: 1997
Title: Determination of the Structure of Alanine Racemase from Bacillus Stearothermophilus at 1.9-A Resolution
Authors: Shaw, J.P. / Petsko, G.A. / Ringe, D.
#2: Journal: J.Biol.Chem. / Year: 1987
Title: X-Ray Crystallographic Studies of the Alanine-Specific Racemase from Bacillus Stearothermophilus. Overproduction, Crystallization, and Preliminary Characterization
Authors: Neidhart, D.J. / Distefano, M.D. / Tanizawa, K. / Soda, K. / Walsh, C.T. / Petsko, G.A.
History
DepositionMay 12, 1998Processing site: BNL
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)87,8444
Polymers87,1322
Non-polymers7122
Water6,972387
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7720 Å2
ΔGint9 kcal/mol
Surface area26460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.227, 87.690, 85.305
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ALANINE RACEMASE


Mass: 43565.953 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Geobacillus stearothermophilus (bacteria) / Plasmid: PMDALR3 / Strain: XL-1 BLUE / References: UniProt: P10724, alanine racemase
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 387 / 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: 2.12 Å3/Da / Density % sol: 41.5 %
Crystal growpH: 8.5
Details: PROTEIN WAS CRYSTALLIZED FROM 100MM TRIS BUFFER, PH 8.5, 200MM SODIUM ACETATE, 21% PEG 4000, AND 4MM 1-AMINOETHYL PHOSPHONIC ACID.
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
130 mg/mlenzyme1drop
221 %(w/v)PEG40001drop
3200 mMsodium acetate1drop
4100 mMTris1drop
5PEG40001reservoir0.700ml

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.15
DetectorType: BRANDEIS / Detector: CCD / Date: Oct 30, 1996 / Details: MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.15 Å / Relative weight: 1
ReflectionResolution: 1.6→25 Å / Num. obs: 97731 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 12.1
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 0.8 / % possible all: 93.7
Reflection
*PLUS
Num. measured all: 516378 / Rmerge F obs: 0.078
Reflection shell
*PLUS
% possible obs: 93.7 %

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SFT

1sft


Resolution: 1.6→10 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.266 2505 6 %RANDOM
Rwork0.24 ---
obs0.24 82763 85 %-
Refinement stepCycle: LAST / Resolution: 1.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6043 0 44 387 6474
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.24
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.752
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2INHIB.PARINHIB2.TOP
X-RAY DIFFRACTION3TOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.24 / Rfactor Rwork: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.752

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