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- PDB-3krv: The Structure Of Potential Metal-Dependent Hydrolase With Cyclase... -

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Basic information

Entry
Database: PDB / ID: 3krv
TitleThe Structure Of Potential Metal-Dependent Hydrolase With Cyclase Activity
ComponentsHydrolase
KeywordsHYDROLASE / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


arylformamidase activity / tryptophan catabolic process to kynurenine / metal ion binding
Similarity search - Function
Putative cyclase / Kynurenine formamidase/cyclase-like / Kynurenine formamidase superfamily / Putative cyclase / Glucose Oxidase; domain 1 / 3-Layer(bba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsRakonjac, N. / Rezacova, P. / Borek, D. / Collart, F. / Joachimiak, A. / Otwinowski, Z. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The Structure Of Potential Metal-Dependent Hydrolase With Cyclase Activity
Authors: Rezacova, P. / Rakonjac, N. / Maderova, J. / Borek, D. / Tomchick, D. / Joachimiak, A. / Collart, F. / Otwinowski, Z.
History
DepositionNov 19, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hydrolase
B: Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,53322
Polymers46,1692
Non-polymers1,36420
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7530 Å2
ΔGint-210 kcal/mol
Surface area16900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.096, 119.096, 124.413
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Hydrolase / / Predicted Metal-Dependent Hydrolase


Mass: 23084.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Plasmid: Pmcsg / Production host: Escherichia coli (E. coli) / References: UniProt: P84132

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Non-polymers , 6 types, 144 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 4.78 Å3/Da / Density % sol: 74.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M LiSulfate, 0.1M TrisH8.5, 1.26M AmmSulfate freezing cond: 20% ethylene glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979 Å
DetectorType: SBC-3 / Detector: CCD / Date: Feb 9, 2007
RadiationMonochromator: double crystal Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 29938 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 8.4 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 39.3
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.688 / Mean I/σ(I) obs: 2.772 / Num. unique all: 2935 / Rsym value: 0.688 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
MOLREPphasing
REFMAC5.3.0037refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R61

1r61


Resolution: 2.55→34.88 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.924 / SU B: 12.079 / SU ML: 0.138 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24435 961 3.2 %RANDOM
Rwork0.19273 ---
obs0.19434 28852 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.582 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20 Å2
2--0.29 Å20 Å2
3----0.59 Å2
Refinement stepCycle: LAST / Resolution: 2.55→34.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3174 0 65 124 3363
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223323
X-RAY DIFFRACTIONr_angle_refined_deg1.6671.9794504
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2985404
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.84523.831154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.10915560
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5581522
X-RAY DIFFRACTIONr_chiral_restr0.1110.2500
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022498
X-RAY DIFFRACTIONr_nbd_refined0.2030.21413
X-RAY DIFFRACTIONr_nbtor_refined0.3130.22235
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2186
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0960.27
X-RAY DIFFRACTIONr_mcbond_it0.9171.52082
X-RAY DIFFRACTIONr_mcangle_it1.51523282
X-RAY DIFFRACTIONr_scbond_it2.50531373
X-RAY DIFFRACTIONr_scangle_it3.9384.51222
LS refinement shellResolution: 2.546→2.612 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.422 66 -
Rwork0.358 2083 -
obs--99.35 %
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)
12.26820.2731-0.40232.875-0.39512.46380.0428-0.12570.01390.0485-0.0735-0.1026-0.04620.0110.03060.15620.037-0.02180.2344-0.010.1568-4.312650.2126-8.6524
20.4065-1.3227-1.34045.0474.76524.63890.16760.3397-0.0948-0.5997-0.0673-0.2945-0.16150.1202-0.10020.3455-0.0024-0.00280.35170.01120.350312.582844.5295-22.7925
30.7024-0.0846-0.52280.6748-0.14160.45210.0350.02460.0838-0.01250.0035-0.0865-0.21790.1589-0.03840.2078-0.0027-0.00360.2087-0.00140.21944.573350.5883-0.9495
40.9914-0.5915-0.09671.9814-0.16171.6405-0.037-0.17590.07870.07210.0596-0.0099-0.00260.0156-0.02260.2201-0.0264-0.00660.1776-0.01050.1689-9.472346.33799.432
50.49810.1967-0.15150.632-0.15260.7195-0.01730.0180.0577-0.01340.00490.0345-0.1214-0.0570.01250.18370.00790.00280.1877-0.00270.2036-12.865155.95914.2245
60.992-0.40230.63221.59-0.36252.07180.0054-0.067-0.0220.05840.01750.01280.0057-0.0122-0.02290.1709-0.00460.00920.2072-0.00660.2065-8.070952.38938.0577
71.18980.17440.56981.33330.62781.96-0.0172-0.00080.0632-0.0825-0.030.1863-0.0225-0.1090.04710.16140.01210.01920.18870.01180.1772-7.662947.90246.0739
83.2422-0.90260.40841.25310.43952.84370.1104-0.1634-0.12460.1484-0.1080.0250.1214-0.105-0.00240.19590.04030.00030.15380.00790.13410.317840.82180.1409
92.75090.27010.48184.03850.19782.34290.0733-0.08070.01180.055-0.07-0.0241-0.07430.0787-0.00340.18630.0468-0.03820.1916-0.030.157412.2135.21210.5954
103.6099-3.0308-1.55065.20261.74542.23580.0578-0.13050.2361-0.01820.041-0.0887-0.1938-0.0563-0.09880.3091-0.0271-0.01620.33610.02390.31518.60348.5784-8.3162
111.8924-0.17760.17511.7797-0.83790.3989-0.0080.2303-0.1401-0.26640.0435-0.01840.0280.0363-0.03540.2067-0.00180.00870.2260.01460.214910.415641.3868-13.5316
120.4521-0.44690.35491.8511-1.20961.2484-0.02550.23160.2151-0.1990.030.0141-0.121-0.0747-0.00460.2739-0.0103-0.00690.2763-0.01780.27511.584330.1854-13.8345
130.4992-0.6537-0.28620.98380.15570.79820.01470.2714-0.3157-0.17940.01320.13130.2202-0.1323-0.02790.2449-0.00250.00220.23630.00710.231113.718417.7512-11.0165
142.05850.2427-0.36441.9570.51411.8224-0.02620.3207-0.2799-0.16090.0954-0.06060.09310.0329-0.06920.27590.02320.0060.23070.03380.243514.518523.5435-15.3849
150.7936-0.3730.03670.65460.25620.57170.00730.1966-0.0544-0.2249-0.0088-0.10810.10550.05130.00140.2075-0.011-0.00360.2048-0.00090.21769.022729.9877-11.7321
166.61354.6944-2.70343.3322-1.91891.1050.031-0.755-1.01630.42780.11210.91250.7047-0.8199-0.14310.3160.0077-0.0010.3023-0.01510.2931-3.144524.59963.9083
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 25
2X-RAY DIFFRACTION2A26 - 38
3X-RAY DIFFRACTION3A39 - 55
4X-RAY DIFFRACTION4A56 - 106
5X-RAY DIFFRACTION5A107 - 132
6X-RAY DIFFRACTION6A133 - 149
7X-RAY DIFFRACTION7A150 - 182
8X-RAY DIFFRACTION8A183 - 203
9X-RAY DIFFRACTION9B0 - 16
10X-RAY DIFFRACTION10B17 - 37
11X-RAY DIFFRACTION11B38 - 56
12X-RAY DIFFRACTION12B57 - 79
13X-RAY DIFFRACTION13B80 - 111
14X-RAY DIFFRACTION14B112 - 140
15X-RAY DIFFRACTION15B141 - 200
16X-RAY DIFFRACTION16B201 - 205

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