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- PDB-1r61: The structure of predicted metal-dependent hydrolase from Bacillu... -

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Basic information

Entry
Database: PDB / ID: 1r61
TitleThe structure of predicted metal-dependent hydrolase from Bacillus stearothermophilus
Componentsmetal-dependent hydrolase
KeywordsHYDROLASE / zinc-dependent hydrolase / structural genomics / cyclase / PSI / 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 / MIRAS / Resolution: 2.5 Å
AuthorsMaderova, J. / Borek, D. / Tomchick, D. / Joachimiak, A. / Collart, F. / Otwinowski, Z. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The structure of potential metal-dependent hydrolase with cyclase activity
Authors: Maderova, J. / Borek, D. / Tomchick, D. / Joachimiak, A. / Collart, F. / Otwinowski, Z.
History
DepositionOct 14, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Mar 13, 2024Group: 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 / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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_conn.ptnr2_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: metal-dependent hydrolase
B: metal-dependent hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,45216
Polymers46,1692
Non-polymers1,28414
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6990 Å2
ΔGint-249 kcal/mol
Surface area17230 Å2
MethodPISA
2
A: metal-dependent hydrolase
B: metal-dependent hydrolase
hetero molecules

A: metal-dependent hydrolase
B: metal-dependent hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,90532
Polymers92,3374
Non-polymers2,56728
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area14960 Å2
ΔGint-509 kcal/mol
Surface area33480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.434, 118.434, 123.542
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-2044-

HOH

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Components

#1: Protein 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
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 3

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Sample preparation

CrystalDensity Matthews: 4.34 Å3/Da / Density % sol: 71.45 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Tris-HCl, ammonium sulphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-BM11.2814
SYNCHROTRONAPS 19-ID20.9196
SYNCHROTRONAPS 19-ID30.9999
Detector
TypeIDDetectorDate
CUSTOM-MADE1CCDApr 21, 2003
CUSTOM-MADE2CCDJun 22, 2003
CUSTOM-MADE3CCDAug 24, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si111SINGLE WAVELENGTHMx-ray1
2Si220SINGLE WAVELENGTHMx-ray1
3Si220SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.28141
20.91961
30.99991
ReflectionResolution: 2.5→35 Å / Num. all: 31141 / Num. obs: 31051 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 34.6
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 5 % / Rmerge(I) obs: 0.833 / Mean I/σ(I) obs: 2.72 / Num. unique all: 1528 / Rsym value: 0.833 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
MLPHAREphasing
DMphasing
ARP/wARPmodel building
RefinementMethod to determine structure: MIRAS / Resolution: 2.5→35 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.946 / SU B: 5.999 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.221 / ESU R Free: 0.193
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21521 1534 5 %RANDOM
Rwork0.17559 ---
all0.17757 28996 --
obs0.17757 28996 98.27 %-
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 mean: 40 Å2
Baniso -1Baniso -2Baniso -3
1-1.92 Å20 Å20 Å2
2--1.92 Å20 Å2
3----3.84 Å2
Refinement stepCycle: LAST / Resolution: 2.5→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3253 0 63 247 3563
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0213378
X-RAY DIFFRACTIONr_bond_other_d0.0010.023056
X-RAY DIFFRACTIONr_angle_refined_deg1.7961.9724593
X-RAY DIFFRACTIONr_angle_other_deg0.86537114
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.0425418
X-RAY DIFFRACTIONr_chiral_restr0.1210.2510
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023714
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02675
X-RAY DIFFRACTIONr_nbd_refined0.2450.2701
X-RAY DIFFRACTIONr_nbd_other0.2710.23732
X-RAY DIFFRACTIONr_nbtor_other0.0960.22110
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.2170
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0860.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3070.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2870.28
X-RAY DIFFRACTIONr_mcbond_it5.64322056
X-RAY DIFFRACTIONr_mcangle_it7.4833337
X-RAY DIFFRACTIONr_scbond_it7.95821322
X-RAY DIFFRACTIONr_scangle_it10.63631251
LS refinement shellResolution: 2.498→2.563 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.363 95
Rwork0.285 1835
obs-1528

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