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- PDB-2sfp: ALANINE RACEMASE WITH BOUND PROPIONATE INHIBITOR -

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Basic information

Entry
Database: PDB / ID: 2sfp
TitleALANINE RACEMASE WITH BOUND PROPIONATE INHIBITOR
ComponentsPROTEIN (ALANINE RACEMASE)
KeywordsRACEMASE / ISOMERASE / ALANINE / PYRIDOXAL PHOSPHATE
Function / homology
Function and homology information


alanine racemase / D-alanine biosynthetic process / alanine racemase activity / pyridoxal phosphate binding
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 / Alanine racemase, N-terminal / Alanine racemase, N-terminal domain / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / 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 / Alanine racemase, N-terminal / Alanine racemase, N-terminal domain / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / 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
PYRIDOXAL-5'-PHOSPHATE / PROPANOIC ACID / Alanine racemase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 1.9 Å
AuthorsMorollo, A.A. / Petsko, G.A. / Ringe, D.
Citation
Journal: Biochemistry / Year: 1999
Title: Structure of a Michaelis complex analogue: propionate binds in the substrate carboxylate site of alanine racemase.
Authors: Morollo, A.A. / Petsko, G.A. / Ringe, D.
#1: 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.
#2: 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.
#3: 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
DepositionFeb 16, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Feb 24, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 6, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / struct_conn
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Aug 30, 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 / struct_conn / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 15, 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: PROTEIN (ALANINE RACEMASE)
B: PROTEIN (ALANINE RACEMASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,0336
Polymers87,3902
Non-polymers6424
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7910 Å2
ΔGint6 kcal/mol
Surface area26720 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)98.700, 90.000, 85.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.8681, 0.1522, -0.4725), (0.1528, -0.8237, -0.5461), (-0.4723, -0.5463, 0.6918)
Vector: 75.617, 94.298, 50.267)

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Components

#1: Protein PROTEIN (ALANINE RACEMASE)


Mass: 43695.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: PYRIDOXAL PHOSPHATE COFACTOR IN ALDIMINE LINKAGE WITH LYS39. CARBOXYLATED LYS129
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Strain: IFO 12550 / Plasmid: PMDALR3 / Species (production host): Escherichia coli / Gene (production host): ALR
Production host: Escherichia coli str. K12 substr. W3110 (bacteria)
Strain (production host): W3110 / References: UniProt: P10724, alanine racemase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-PPI / PROPANOIC ACID / Propionic acid


Mass: 74.079 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsPLP: THE ALDEHYDE FORMED BY O4 AS LISTED IN THE HET GROUP DICTIONARY IS NOT PRESENT IN THIS ENTRY ...PLP: THE ALDEHYDE FORMED BY O4 AS LISTED IN THE HET GROUP DICTIONARY IS NOT PRESENT IN THIS ENTRY DUE TO FORMATION OF THE ALDIMINE WITH NZ OF LYS 39.

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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: 2.16 Å3/Da / Density % sol: 43.16 %
Crystal growpH: 8.5 / Details: pH 8.50
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlprotein1drop
2100 mMTris-HCl1drop
3200 mMsodium acetate1drop
40.01 MPLP1drop
50.1 %BME1drop
620-22 %PEG40001reservoir
7200 mMsodium acetate1reservoir
80.01 MPLP1reservoir
90.01 %BME1reservoir
10100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 296 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Mar 1, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 52775 / % possible obs: 87 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 15.1
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 1.7 / % possible all: 54.8
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 30 Å / % possible obs: 87 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Num. measured all: 178589
Reflection shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 1.97 Å / % possible obs: 54.8 % / Redundancy: 1.6 % / Mean I/σ(I) obs: 1.7

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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: OTHER
Starting model: 1SFT

1sft


Resolution: 1.9→10 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1889 3.1 %RANDOM
Rwork0.205 ---
obs-49777 82.9 %-
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6032 0 40 207 6279
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_deg1.37
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.71
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
LS refinement shellResolution: 1.9→1.99 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.349 135 1.8 %
Rwork0.313 3465 -
obs--48.5 %
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 10 Å / σ(F): 0 / % reflection Rfree: 3.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.71
LS refinement shell
*PLUS
Rfactor obs: 0.313

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