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- PDB-3h12: Crystal structure of putative mandelate racemase from Bordetella ... -

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Basic information

Entry
Database: PDB / ID: 3h12
TitleCrystal structure of putative mandelate racemase from Bordetella Bronchiseptica RB50
Componentsmandelate racemase
KeywordsISOMERASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / enolase / 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/muconate lactonizing enzyme, conserved site / Mandelate racemase DgoD-like / 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/muconate lactonizing enzyme, conserved site / Mandelate racemase DgoD-like / 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
Mandelate racemase / Putative mandelate racemase
Similarity search - Component
Biological speciesBordetella bronchiseptica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsMalashkevich, V.N. / Toro, R. / Morano, C. / 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
Authors: Malashkevich, V.N. / Toro, R. / Morano, C. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionApr 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 24, 2012Group: Structure summary
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.5Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: mandelate racemase
B: mandelate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9684
Polymers86,9222
Non-polymers462
Water14,070781
1
A: mandelate racemase
B: mandelate racemase
hetero molecules

A: mandelate racemase
B: mandelate racemase
hetero molecules

A: mandelate racemase
B: mandelate racemase
hetero molecules

A: mandelate racemase
B: mandelate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)347,87316
Polymers347,6898
Non-polymers1848
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area40630 Å2
ΔGint-164 kcal/mol
Surface area87140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.148, 116.148, 128.136
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-861-

HOH

21B-865-

HOH

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Components

#1: Protein mandelate racemase /


Mass: 43461.117 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 781 / 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: 2.49 Å3/Da / Density % sol: 50.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.8 M Na-acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 24, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionRedundancy: 2.4 % / Av σ(I) over netI: 20.57 / Number: 587240 / Rmerge(I) obs: 0.053 / Χ2: 1.46 / D res high: 1.49 Å / D res low: 50 Å / Num. obs: 240271 / % possible obs: 88.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.045085.210.0251.4882.8
3.214.048610.031.6642.7
2.83.2187.510.0411.9792.7
2.552.888.810.0532.0922.7
2.372.5589.410.061.8562.7
2.232.379010.0711.8642.6
2.112.2390.310.0821.8722.5
2.022.1190.610.1011.8342.5
1.942.029110.1241.572.4
1.881.9491.110.161.5292.4
1.821.8891.110.191.3892.4
1.771.8291.310.2251.2522.4
1.721.7791.410.2811.0942.4
1.681.7291.910.3321.042.3
1.641.6891.410.3960.9982.3
1.611.6491.710.4640.9672.3
1.571.6191.310.5530.9662.3
1.541.579010.5980.8722.2
1.521.5484.510.7110.9212.1
1.491.5269.910.7850.872
ReflectionResolution: 1.49→50 Å / Num. obs: 240271 / % possible obs: 88.7 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.053 / Χ2: 1.457 / Net I/σ(I): 20.574
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.49-1.5220.78594590.87169.9
1.52-1.542.10.711114120.921184.5
1.54-1.572.20.598122300.872190
1.57-1.612.30.553123710.966191.3
1.61-1.642.30.464123660.967191.7
1.64-1.682.30.396124830.998191.4
1.68-1.722.30.332123801.04191.9
1.72-1.772.40.281123801.094191.4
1.77-1.822.40.225123771.252191.3
1.82-1.882.40.19123411.389191.1
1.88-1.942.40.16122711.529191.1
1.94-2.022.40.124123801.57191
2.02-2.112.50.101122301.834190.6
2.11-2.232.50.082122311.872190.3
2.23-2.372.60.071122351.864190
2.37-2.552.70.06120471.856189.4
2.55-2.82.70.053120542.092188.8
2.8-3.212.70.041118281.979187.5
3.21-4.042.70.03116561.664186
4.04-502.80.025115401.488185.2

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
CBASSdata collection
HKL-2000data reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→8.73 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.973 / WRfactor Rfree: 0.164 / WRfactor Rwork: 0.138 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.908 / SU B: 2.475 / SU ML: 0.04 / SU R Cruickshank DPI: 0.061 / SU Rfree: 0.064 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.173 6483 5 %RANDOM
Rwork0.146 ---
obs0.147 128899 95.77 %-
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: 204.68 Å2 / Biso mean: 19.986 Å2 / Biso min: 8.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.5→8.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6026 0 2 781 6809
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.0216214
X-RAY DIFFRACTIONr_angle_refined_deg2.4531.9418449
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5935792
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.38323.436291
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.65515997
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8441552
X-RAY DIFFRACTIONr_chiral_restr0.2030.2921
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0214814
X-RAY DIFFRACTIONr_mcbond_it1.5723.53900
X-RAY DIFFRACTIONr_mcangle_it3.971506221
X-RAY DIFFRACTIONr_scbond_it7.928502314
X-RAY DIFFRACTIONr_scangle_it2.9874.52224
LS refinement shellResolution: 1.5→1.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 449 -
Rwork0.318 8571 -
all-9020 -
obs--92.97 %
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)
10.2172-0.00380.00690.16410.03370.2776-0.0131-0.0122-0.04580.0177-0.00550.01920.0444-0.02340.01860.0143-0.00480.01120.0032-0.00060.015742.875629.16627.7869
20.16370.0001-0.04120.2334-0.00930.2417-0.00730.0275-0.0013-0.0204-0.00770.04210.0247-0.04890.0150.0045-0.0052-0.00190.0193-0.00910.012127.697745.34851.9409
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 393
2X-RAY DIFFRACTION1A500
3X-RAY DIFFRACTION1A398 - 895
4X-RAY DIFFRACTION2B2 - 393
5X-RAY DIFFRACTION2B500
6X-RAY DIFFRACTION2B398 - 894

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