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- PDB-3fv9: Crystal structure of putative mandelate racemase/muconatelactoniz... -

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Entry
Database: PDB / ID: 3fv9
TitleCrystal structure of putative mandelate racemase/muconatelactonizing enzyme from ROSEOVARIUS NUBINHIBENS ISM complexed with magnesium
ComponentsMandelate racemase/muconate lactonizing enzyme
KeywordsHYDROLASE / STRUCTURAL GENOMICS / MANDELATE RACEMASE/MUCONATELACTONIZING ENZYME / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


catalytic activity / metal ion binding
Similarity search - Function
Mandelate racemase DgoD-like / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-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 ...Mandelate racemase DgoD-like / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-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/muconate lactonizing enzyme, putative
Similarity search - Component
Biological speciesRoseovarius nubinhibens ISM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsMalashkevich, V.N. / Rutter, M. / Bain, K.T. / Lau, C. / Ozyurt, S. / Smith, D. / Wasserman, S. / 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/muconatelactonizing enzyme from ROSEOVARIUS NUBINHIBENS ISM complexed with magnesium
Authors: Malashkevich, V.N. / Rutter, M. / Bain, K.T. / Lau, C. / Ozyurt, S. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionJan 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2Oct 24, 2012Group: Structure summary
Revision 1.3Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / 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 / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.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 1.5Feb 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

Downloads & links

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Assembly

Deposited unit
G: Mandelate racemase/muconate lactonizing enzyme
A: Mandelate racemase/muconate lactonizing enzyme
D: Mandelate racemase/muconate lactonizing enzyme
E: Mandelate racemase/muconate lactonizing enzyme
F: Mandelate racemase/muconate lactonizing enzyme
B: Mandelate racemase/muconate lactonizing enzyme
H: Mandelate racemase/muconate lactonizing enzyme
C: Mandelate racemase/muconate lactonizing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)328,92813
Polymers328,8068
Non-polymers1225
Water46,8392600
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29130 Å2
ΔGint-145 kcal/mol
Surface area84600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.082, 174.566, 108.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21C
31D
41E
51F
61G
71H
81A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Refine code: 1 / Auth seq-ID: -99999 - 99999 / Label seq-ID: -99999 - 99999

Dom-IDAuth asym-IDLabel asym-ID
1BB
2CC
3DD
4EE
5FF
6GG
7HH
8AA

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Components

#1: Protein
Mandelate racemase/muconate lactonizing enzyme


Mass: 41100.797 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Roseovarius nubinhibens ISM (bacteria) / Gene: ISM_14080 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: A3SNG0
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2600 / 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: 2.44 Å3/Da / Density % sol: 49.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 24% PEG3350, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9791 Å
DetectorType: MAR scanner 180 mm plate / Detector: IMAGE PLATE
RadiationProtocol: SAD / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.9→46.094 Å / Num. obs: 240078 / % possible obs: 95.9 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 7.619
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.9-2.0110.90.3781.5363082333280.37892.1
2.01-2.1312.30.2343404361327840.23495.4
2.13-2.2712.20.1764375063306740.17695.1
2.27-2.4612.20.1325.3348266284630.13294.6
2.46-2.6912.20.1046.7321437264170.10495.3
2.69-3.0112.10.088.4295572244400.0897.1
3.01-3.4712.20.06110.3269546220210.06198.7
3.47-4.2512.70.04812.6239194187940.04899.2
4.25-6.0214.20.04413.7209768148210.044100
6.02-46.0914.10.04112.811713083360.04199.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 41.99 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å46.09 Å
Translation2.5 Å46.09 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.906 / WRfactor Rwork: 1.01 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.799 / SU B: 8.138 / SU ML: 0.105 / SU R Cruickshank DPI: 0.174 / SU Rfree: 0.156 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.241 12030 5 %RANDOM
Rwork0.203 ---
obs0.205 239777 95.73 %-
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: 72.81 Å2 / Biso mean: 18.525 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: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22009 0 5 2600 24614
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02122451
X-RAY DIFFRACTIONr_angle_refined_deg1.1831.97530506
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.34852972
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.42222.503887
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.237153658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9115236
X-RAY DIFFRACTIONr_chiral_restr0.0710.23531
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02116948
X-RAY DIFFRACTIONr_mcbond_it0.6793.514718
X-RAY DIFFRACTIONr_mcangle_it2.4515023445
X-RAY DIFFRACTIONr_scbond_it5.657507733
X-RAY DIFFRACTIONr_scangle_it0.8374.57056
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2642 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
BTIGHT POSITIONAL0.665
CTIGHT POSITIONAL0.425
DTIGHT POSITIONAL0.685
ETIGHT POSITIONAL0.365
FTIGHT POSITIONAL0.555
GTIGHT POSITIONAL0.395
HTIGHT POSITIONAL0.345
ATIGHT POSITIONAL0.45
BTIGHT THERMAL2.1910
CTIGHT THERMAL1.6510
DTIGHT THERMAL1.9510
ETIGHT THERMAL1.9110
FTIGHT THERMAL2.5510
GTIGHT THERMAL2.2910
HTIGHT THERMAL2.7910
ATIGHT THERMAL1.7410
LS refinement shellResolution: 1.9→1.952 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.427 848 -
Rwork0.424 15329 -
all-16177 -
obs--88.87 %
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)
10.6055-0.0643-0.0030.5573-0.0740.3873-0.04440.1220.0727-0.07570.02950.0806-0.0097-0.02070.01490.0194-0.0076-0.02220.04290.01520.026714.7839-29.5035-44.5055
20.6426-0.26160.10030.7569-0.0660.2263-0.0072-0.074-0.12610.16340-0.02510.05760.00780.00720.08040.015-0.00730.03070.02510.037853.9497-68.7633-12.8339
30.53350.0371-0.03570.59160.04060.2346-0.0283-0.04790.08430.2-0.0414-0.155-0.05040.03030.06970.1295-0.025-0.10760.04630.02790.105169.6618-26.5379-8.7348
40.6005-0.37590.01330.8244-0.15960.225-0.0731-0.0890.13370.22160.04850.0162-0.0595-0.00530.02460.10050.0237-0.0120.0221-0.03130.069927.7162-9.8229-15.7241
50.69040.12270.11410.5392-0.20980.37330.0081-0.0727-0.05160.07520.01380.0885-0.0071-0.0633-0.02190.021-0.00890.02310.0261-0.00150.031711.3613-52.4938-19.0255
60.6390.12890.16660.6232-0.04940.20930.03730.1716-0.1899-0.0520.0040.01160.06050.045-0.04140.0430.0136-0.0070.0598-0.05950.065935.1246-69.7198-41.6943
70.5612-0.10710.27481.2749-0.03670.32910.02590.16050.0202-0.0979-0.0553-0.35990.0440.14330.02940.01850.03570.03630.11770.03670.109875.2337-48.7207-34.4134
80.30850.1091-0.14190.99880.16230.4531-0.03940.06380.1048-0.0303-0.0084-0.1021-0.07070.03750.04770.0303-0.0205-0.04320.04890.05570.102454.4477-8.227-37.4206
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B1 - 373
2X-RAY DIFFRACTION1B501
3X-RAY DIFFRACTION2C1 - 374
4X-RAY DIFFRACTION2C501
5X-RAY DIFFRACTION3D1 - 373
6X-RAY DIFFRACTION4E1 - 373
7X-RAY DIFFRACTION4E501
8X-RAY DIFFRACTION5F1 - 373
9X-RAY DIFFRACTION5F501
10X-RAY DIFFRACTION6G1 - 373
11X-RAY DIFFRACTION6G385 - 2984
12X-RAY DIFFRACTION7H1 - 374
13X-RAY DIFFRACTION8A1 - 374
14X-RAY DIFFRACTION8A501

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