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- PDB-3dfh: crystal structure of putative mandelate racemase / muconate lacto... -

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Basic information

Entry
Database: PDB / ID: 3dfh
Titlecrystal structure of putative mandelate racemase / muconate lactonizing enzyme from Vibrionales bacterium SWAT-3
Componentsmandelate racemase
KeywordsISOMERASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / putative mandelate racemase / muconate lactonizing enzyme / PSI-2 / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


amino acid catabolic process / magnesium ion binding
Similarity search - Function
D-mannonate dehydratase-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 ...D-mannonate dehydratase-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
D-galactonate dehydratase family member VSWAT3_13707
Similarity search - Component
Biological speciesVibrionales bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsMalashkevich, V.N. / Toro, R. / Wasserman, S.R. / Meyer, A.J. / 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 / muconate lactonizing enzyme from Vibrionales bacterium SWAT-3
Authors: Malashkevich, V.N. / Toro, R. / Wasserman, S.R. / Meyer, A.J. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionJun 12, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 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 1.3Nov 14, 2018Group: Data collection / Derived calculations / Structure summary
Category: audit_author / pdbx_struct_special_symmetry / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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 1.5Feb 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)134,2526
Polymers134,1833
Non-polymers693
Water6,756375
1
C: mandelate racemase
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)358,00516
Polymers357,8218
Non-polymers1848
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_556-x,y,-z+11
crystal symmetry operation6_556x,-y,-z+11
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_556-y,-x,-z+11
Buried area37380 Å2
ΔGint-26 kcal/mol
Surface area85250 Å2
MethodPISA
2
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)358,00516
Polymers357,8218
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 area37350 Å2
ΔGint-34 kcal/mol
Surface area85210 Å2
MethodPISA
3
A: mandelate racemase
hetero molecules

B: mandelate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,5014
Polymers89,4552
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-y+1,x,z1
Buried area3590 Å2
ΔGint-12 kcal/mol
Surface area27050 Å2
MethodPISA
4
C: mandelate racemase
hetero molecules

C: mandelate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,5014
Polymers89,4552
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area3610 Å2
ΔGint-11 kcal/mol
Surface area27050 Å2
MethodPISA
5
A: mandelate racemase
B: mandelate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,5014
Polymers89,4552
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-4 kcal/mol
Surface area27890 Å2
MethodPISA
6
C: mandelate racemase
hetero molecules

C: mandelate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,5014
Polymers89,4552
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_556x,-y,-z+11
Buried area2730 Å2
ΔGint-4 kcal/mol
Surface area27930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.836, 121.836, 319.347
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-502-

NA

21B-503-

NA

31C-501-

NA

41A-541-

HOH

51B-659-

HOH

61B-665-

HOH

71C-626-

HOH

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Components

#1: Protein mandelate racemase


Mass: 44727.594 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrionales bacterium (bacteria) / Strain: SWAT-3 / Gene: VSWAT3_13707 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: A5KUH4
#2: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 375 / 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: 2.21 Å3/Da / Density % sol: 44.29 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M MES, 35% MPD, 0.2 M lithium sulfate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 29, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionRedundancy: 7.9 % / Av σ(I) over netI: 8.5 / Number: 919884 / Rmerge(I) obs: 0.092 / Χ2: 1.38 / D res high: 2.2 Å / D res low: 50 Å / Num. obs: 116723 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.745099.910.0391.9118
3.764.7410010.0551.9767.7
3.293.7610010.0852.4247.8
2.993.2910010.1061.567.9
2.772.9910010.1411.1088
2.612.7710010.191.0118
2.482.6110010.2680.9687.9
2.372.4810010.3630.9677.9
2.282.3710010.4630.9477.8
2.22.2810010.6250.9367.8
ReflectionResolution: 2.2→50 Å / Num. obs: 116723 / % possible obs: 100 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.092 / Χ2: 1.38 / Net I/σ(I): 8.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.2-2.287.80.625116520.9361100
2.28-2.377.80.463116950.9471100
2.37-2.487.90.363116960.9671100
2.48-2.617.90.268116510.9681100
2.61-2.7780.19116601.0111100
2.77-2.9980.141116811.1081100
2.99-3.297.90.106116601.561100
3.29-3.767.80.085116502.4241100
3.76-4.747.70.055116821.9761100
4.74-5080.039116961.911199.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→41.59 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.834 / SU B: 12.279 / SU ML: 0.142 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.246 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.234 3113 5.1 %RANDOM
Rwork0.173 ---
obs0.176 61155 100 %-
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 max: 79.92 Å2 / Biso mean: 25.051 Å2 / Biso min: 2.15 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.2→41.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8571 0 3 375 8949
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0228791
X-RAY DIFFRACTIONr_angle_refined_deg1.6761.93711939
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.48451073
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.05624.839436
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.023151466
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.4131539
X-RAY DIFFRACTIONr_chiral_restr0.1090.21300
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216770
X-RAY DIFFRACTIONr_mcbond_it1.2133.55361
X-RAY DIFFRACTIONr_mcangle_it4.12508673
X-RAY DIFFRACTIONr_scbond_it9.341503430
X-RAY DIFFRACTIONr_scangle_it1.5164.53265
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 218 -
Rwork0.19 4252 -
all-4470 -
obs--100 %
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)
10.65470.4545-0.11211.1531-0.12840.7088-0.01690.113-0.1674-0.04370.1156-0.08750.15440.06-0.0986-0.02940.0243-0.0506-0.0561-0.0467-0.053355.310928.881693.2122
20.75890.4652-0.0490.8453-0.00120.56010.0467-0.03670.04450.11470.07180.1726-0.0133-0.1375-0.1185-0.0530.01360.0399-0.02340.0971-0.046733.252343.8737118.7377
31.05650.11510.14050.5589-0.16010.85-0.07950.0770.1116-0.0313-0.0921-0.1462-0.12490.17570.1716-0.0819-0.0516-0.0028-0.03580.13290.012529.66313.2679146.921
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 380
2X-RAY DIFFRACTION2B2 - 380
3X-RAY DIFFRACTION3C2 - 380

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