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- PDB-3op2: Crystal structure of putative mandelate racemase from Bordetella ... -

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Basic information

Entry
Database: PDB / ID: 3op2
TitleCrystal structure of putative mandelate racemase from Bordetella bronchiseptica RB50 complexed with 2-oxoglutarate/phosphate
ComponentsPutative mandelate racemase
KeywordsISOMERASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / racemase / 2-oxoglutarate / PSI-2 / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


amino acid catabolic process / hydro-lyase activity / metal ion binding
Similarity search - Function
: / Mandelate racemase / muconate lactonizing enzyme family signature 1. / Mandelate racemase DgoD-like / Mandelate racemase/muconate lactonizing enzyme, conserved site / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like ...: / Mandelate racemase / muconate lactonizing enzyme family signature 1. / Mandelate racemase DgoD-like / Mandelate racemase/muconate lactonizing enzyme, conserved site / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Enolase-like; domain 1 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / PHOSPHATE ION / Mandelate racemase / Putative mandelate racemase
Similarity search - Component
Biological speciesBordetella bronchiseptica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsMalashkevich, V.N. / Patskovsky, Y. / Ramagopal, U. / Toro, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of putative mandelate racemase from Bordetella bronchiseptica RB50 complexed with 2-oxoglutarate/phosphate
Authors: Malashkevich, V.N. / Patskovsky, Y. / Ramagopal, U. / Toro, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionAug 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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.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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Dec 6, 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: Putative mandelate racemase
B: Putative mandelate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,1506
Polymers87,8602
Non-polymers2904
Water7,260403
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-35 kcal/mol
Surface area28500 Å2
Unit cell
Length a, b, c (Å)117.550, 117.550, 123.210
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Putative mandelate racemase /


Mass: 43930.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella bronchiseptica (bacteria) / Strain: RB50 / Gene: BB4687 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: Q7WEE8, UniProt: A0A0H3LT39*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 403 / 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: 2.42 Å3/Da / Density % sol: 49.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.8 M sodium acetate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 19, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 56531 / % possible obs: 99.9 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.111 / Χ2: 0.989 / Net I/σ(I): 7.6
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2% possible allRmerge(I) obs
2-2.036.628060.69999.7
2.03-2.077.528480.976100
2.07-2.117.528030.8511000.98
2.11-2.157.528330.7571000.779
2.15-2.27.628120.781000.655
2.2-2.257.528391.1691000.595
2.25-2.317.627920.9241000.52
2.31-2.377.627760.8521000.405
2.37-2.447.728300.8741000.349
2.44-2.527.728440.9341000.276
2.52-2.617.728020.9661000.246
2.61-2.717.728401.11000.215
2.71-2.847.828101.0111000.163
2.84-2.997.828351.0151000.142
2.99-3.177.828231.0671000.114
3.17-3.427.828401.041000.091
3.42-3.767.728261.2671000.085
3.76-4.317.728481.26199.80.077
4.31-5.437.628331.02499.80.068
5.43-507.828911.13399.70.081

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H12
Resolution: 2→19.99 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.2188 / WRfactor Rwork: 0.1821 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.8446 / SU B: 9.818 / SU ML: 0.122 / SU R Cruickshank DPI: 0.22 / SU Rfree: 0.1785 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.22 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2223 2389 5.1 %RANDOM
Rwork0.1834 ---
obs0.1854 47085 83.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 79.43 Å2 / Biso mean: 32.063 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5728 0 17 403 6148
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225893
X-RAY DIFFRACTIONr_angle_refined_deg1.1731.9478019
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9345744
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.16823.686274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.27915937
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4331547
X-RAY DIFFRACTIONr_chiral_restr0.080.2886
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214547
X-RAY DIFFRACTIONr_mcbond_it0.8843.53695
X-RAY DIFFRACTIONr_mcangle_it3.36505905
X-RAY DIFFRACTIONr_scbond_it8.287502198
X-RAY DIFFRACTIONr_scangle_it0.8364.52111
LS refinement shellResolution: 2.003→2.055 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.138 6 -
Rwork0.175 138 -
all-144 -
obs--3.51 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.68090.1669-0.16850.3997-0.11150.4394-0.01040.0699-0.0793-0.0735-0.01220.05350.0517-0.09220.02260.0175-0.0012-0.01280.0606-0.04390.04527.490947.6498-28.2765
20.54480.0420.09720.68610.45590.7624-0.0593-0.0689-0.09450.04740.00780.10150.0789-0.06440.05150.0532-0.01070.03580.0210.00870.042343.065829.7494-2.1045
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999

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