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- PDB-3oo2: 2.37 Angstrom resolution crystal structure of an alanine racemase... -

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Basic information

Entry
Database: PDB / ID: 3oo2
Title2.37 Angstrom resolution crystal structure of an alanine racemase (alr) from Staphylococcus aureus subsp. aureus COL
ComponentsAlanine racemase 1
KeywordsISOMERASE / Alanine Racemase / Infectious Diseases / Center for Structural Genomics of Infectious Diseases (CSGID) / Alanine and Aspartate Metabolism and D-alanine Metabolism / Biosynthesis and degradation of murein sacculus and peptidoglycan
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
BETA-MERCAPTOETHANOL / PHOSPHATE ION / Alanine racemase 1
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsHalavaty, A.S. / Shuvalova, L. / Minasov, G. / Winsor, J. / Dubrovska, I. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 2.37 Angstrom resolution crystal structure of an alanine racemase (alr) from Staphylococcus aureus subsp. aureus COL
Authors: Halavaty, A.S. / Shuvalova, L. / Minasov, G. / Winsor, J. / Dubrovska, I. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionAug 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Apr 3, 2024Group: 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_conn_type / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_type.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: Alanine racemase 1
B: Alanine racemase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,7659
Polymers86,2952
Non-polymers4707
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7200 Å2
ΔGint-59 kcal/mol
Surface area28260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.735, 118.310, 129.008
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 1 /


Mass: 43147.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: COL / Gene: alr, alr1, SACOL2060 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/Magic / References: UniProt: Q5HED1, alanine racemase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.11 Å3/Da / Density % sol: 41.73 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 7.6 mg/mL protein in 10 mM Tris/HCl pH 8.3, 0.5 M NaCl, 5 mM BME. Crystals grew from 0.1 M MIB buffer pH 5.0, 25 % (w/v) PEG1500 (The PACT suite condition #14), VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 7, 2010 / Details: Be-Lenses/Diamond Laue Mono
RadiationMonochromator: Diamond[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.37→30 Å / Num. all: 30323 / Num. obs: 30323 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 18.36
Reflection shellResolution: 2.37→2.41 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.572 / Mean I/σ(I) obs: 2.66 / Num. unique all: 1494 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
BALBESphasing
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Balbes model

Resolution: 2.37→29.59 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.903 / SU B: 19.971 / SU ML: 0.218 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.285 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25683 1533 5.1 %RANDOM
Rwork0.19972 ---
obs0.20259 28741 99.52 %-
all-28741 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 53.394 Å2
Baniso -1Baniso -2Baniso -3
1-1.52 Å2-0 Å20 Å2
2---1.62 Å2-0 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.37→29.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5866 0 24 120 6010
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0226051
X-RAY DIFFRACTIONr_bond_other_d0.0010.024049
X-RAY DIFFRACTIONr_angle_refined_deg1.5671.9568196
X-RAY DIFFRACTIONr_angle_other_deg0.83539932
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.0075750
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.90524.689273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.545151081
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6231530
X-RAY DIFFRACTIONr_chiral_restr0.0950.2933
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026682
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021160
X-RAY DIFFRACTIONr_mcbond_it1.1051.53731
X-RAY DIFFRACTIONr_mcbond_other0.2991.51513
X-RAY DIFFRACTIONr_mcangle_it1.94926058
X-RAY DIFFRACTIONr_scbond_it3.31732320
X-RAY DIFFRACTIONr_scangle_it4.854.52138
LS refinement shellResolution: 2.372→2.433 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 103 -
Rwork0.258 2042 -
obs-2042 99.08 %
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)
11.15870.8539-0.18292.12010.29761.4655-0.21720.1787-0.0096-0.25630.02460.2592-0.0687-0.19870.19250.0651-0.0417-0.05020.1110.02250.1167-12.635853.2467-10.2212
21.05950.4976-0.11012.56671.3321.745-0.24990.3557-0.049-0.53330.2619-0.0976-0.24690.1609-0.0120.1352-0.09630.02910.18530.00910.02013.842458.3328-14.2222
31.65080.29550.32351.71290.67371.6845-0.08980.13230.2106-0.27880.1037-0.1884-0.43970.1999-0.0140.1454-0.0883-0.01050.08160.05120.09249.082373.84420.4201
41.28780.78710.55743.75781.20691.12370.0073-0.22010.19750.1084-0.29440.4285-0.0934-0.3360.28710.05450.0132-0.01470.1728-0.04820.1026-4.711275.814619.6582
54.6551-2.46590.18694.9371-0.61574.5033-0.0913-0.14440.65520.668-0.1613-0.53450.10540.24530.25260.2075-0.0799-0.10910.15570.02030.174410.567385.782728.0407
61.43480.30960.5672.59311.29461.87720.0684-0.1267-0.19750.4174-0.06680.00370.2058-0.0013-0.00160.0746-0.0326-0.02020.07110.06940.07492.135453.041713.8799
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 174
2X-RAY DIFFRACTION2A175 - 269
3X-RAY DIFFRACTION3A270 - 382
4X-RAY DIFFRACTION4B2 - 133
5X-RAY DIFFRACTION5B134 - 200
6X-RAY DIFFRACTION6B201 - 382

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