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- PDB-4wgx: Crystal Structure of Molinate Hydrolase -

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Basic information

Entry
Database: PDB / ID: 4wgx
TitleCrystal Structure of Molinate Hydrolase
ComponentsMolinate hydrolase
KeywordsHYDROLASE / Amidohydrolase
Function / homology
Function and homology information


hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
Similarity search - Function
Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel / Alpha-Beta Barrel ...Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / Molinate hydrolase
Similarity search - Component
Biological speciesGulosibacter molinativorax (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.29 Å
AuthorsSugrue, E. / Carr, P.D. / Fraser, N.J. / Hopkins, D.H. / Jackson, C.J.
CitationJournal: Appl.Environ.Microbiol. / Year: 2015
Title: Evolutionary Expansion of the Amidohydrolase Superfamily in Bacteria in Response to the Synthetic Compounds Molinate and Diuron.
Authors: Sugrue, E. / Fraser, N.J. / Hopkins, D.H. / Carr, P.D. / Khurana, J.L. / Oakeshott, J.G. / Scott, C. / Jackson, C.J.
History
DepositionSep 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 18, 2015Group: Derived calculations
Revision 1.2Mar 25, 2015Group: Database references
Revision 1.3Sep 6, 2017Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: citation / diffrn_detector ...citation / diffrn_detector / diffrn_source / entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _diffrn_detector.detector ..._citation.journal_id_CSD / _diffrn_detector.detector / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.4Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.5Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.6Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Molinate hydrolase
B: Molinate hydrolase
C: Molinate hydrolase
D: Molinate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,93215
Polymers203,9284
Non-polymers1,00411
Water13,799766
1
A: Molinate hydrolase
B: Molinate hydrolase
hetero molecules

A: Molinate hydrolase
B: Molinate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,22718
Polymers203,9284
Non-polymers1,29914
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_455-x-1/2,y,-z1
Buried area15040 Å2
ΔGint-166 kcal/mol
Surface area59950 Å2
MethodPISA
2
C: Molinate hydrolase
D: Molinate hydrolase
hetero molecules

C: Molinate hydrolase
D: Molinate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,63712
Polymers203,9284
Non-polymers7088
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x,-y,-z+1/21
Buried area13890 Å2
ΔGint-117 kcal/mol
Surface area60140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.429, 226.317, 265.382
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11B-630-

HOH

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Components

#1: Protein
Molinate hydrolase


Mass: 50982.074 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gulosibacter molinativorax (bacteria) / Gene: molA / Plasmid: pETcc2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G2XLB0
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Co
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 766 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.64 Å3/Da / Density % sol: 73.5 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Microcrystals obtained in 45 % MPD, 0.2 M ammonium acetate, 0.1 M BIS-Tris pH 6 were used as microseeds to create larger crystals in 48 % MPD, 0.2 M ammonium acetate, 0.1 M BIS-Tris pH 6.0.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.29→63.165 Å / Num. all: 170085 / Num. obs: 170085 / % possible obs: 99.9 % / Redundancy: 20.3 % / Rmerge(I) obs: 0.182 / Net I/σ(I): 16.3
Reflection shellResolution: 2.29→2.33 Å / Redundancy: 13.5 % / Mean I/σ(I) obs: 1.6 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementResolution: 2.29→41.621 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2032 8551 5.03 %
Rwork0.176 161383 -
obs0.1774 169934 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 183.56 Å2 / Biso mean: 51.0019 Å2 / Biso min: 15.29 Å2
Refinement stepCycle: final / Resolution: 2.29→41.621 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14296 0 137 766 15199
Biso mean--84.18 41.02 -
Num. residues----1860
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00814711
X-RAY DIFFRACTIONf_angle_d1.18819987
X-RAY DIFFRACTIONf_chiral_restr0.0442266
X-RAY DIFFRACTIONf_plane_restr0.0052621
X-RAY DIFFRACTIONf_dihedral_angle_d15.4165417
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.29-2.3160.33312910.29835230552199
2.316-2.34330.30762800.289253205600100
2.3433-2.37180.33962890.287853255614100
2.3718-2.40190.30862780.27353155593100
2.4019-2.43350.28723000.257953555655100
2.4335-2.46680.27822910.248753045595100
2.4668-2.5020.28212980.246753565654100
2.502-2.53940.27452820.232653565638100
2.5394-2.5790.26622840.235253725656100
2.579-2.62130.26462540.228953295583100
2.6213-2.66650.26792610.224253515612100
2.6665-2.7150.24773180.218553325650100
2.715-2.76720.26742630.214654055668100
2.7672-2.82370.23772990.212653355634100
2.8237-2.88510.24422870.20953365623100
2.8851-2.95220.2442710.202954025673100
2.9522-3.0260.23742540.199653775631100
3.026-3.10780.23192980.194953435641100
3.1078-3.19920.21723110.189553805691100
3.1992-3.30240.242920.194653695661100
3.3024-3.42040.21092930.183953715664100
3.4204-3.55720.2072700.167653855655100
3.5572-3.7190.17942990.156954025701100
3.719-3.9150.17692750.147553955670100
3.915-4.16010.1572610.137254305691100
4.1601-4.48090.1552970.127754015698100
4.4809-4.93120.1432940.124754405734100
4.9312-5.64320.14752470.140355115758100
5.6432-7.10410.17382950.166955135808100
7.1041-41.62830.16793190.147356435962100

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