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- PDB-3gor: Crystal structure of putative metal-dependent hydrolase APC36150 -

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Basic information

Entry
Database: PDB / ID: 3gor
TitleCrystal structure of putative metal-dependent hydrolase APC36150
ComponentsPutative metal-dependent hydrolase
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / DinB Superfamily / PSI-2 / Protein Structure Initiative / Integrated Center for Structure and Function Innovation / ISFI
Function / homologyDNA damage-inducible protein DinB / DinB family / dinb family like domain / DinB/YfiT-like putative metalloenzymes / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / NICKEL (II) ION / Putative metal-dependent hydrolase
Function and homology information
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / MAD / Resolution: 2.511 Å
AuthorsCooper, D.R. / Grelewska, K. / Derewenda, Z.S. / Integrated Center for Structure and Function Innovation (ISFI)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: The structure of DinB from Geobacillus stearothermophilus: a representative of a unique four-helix-bundle superfamily.
Authors: Cooper, D.R. / Grelewska, K. / Kim, C.Y. / Joachimiak, A. / Derewenda, Z.S.
History
DepositionMar 19, 2009Deposition site: RCSB / Processing site: RCSB
SupersessionMay 19, 2009ID: 3E4X
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative metal-dependent hydrolase
B: Putative metal-dependent hydrolase
C: Putative metal-dependent hydrolase
D: Putative metal-dependent hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7548
Polymers74,5204
Non-polymers2354
Water1,04558
1
A: Putative metal-dependent hydrolase
B: Putative metal-dependent hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3774
Polymers37,2602
Non-polymers1172
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Putative metal-dependent hydrolase
D: Putative metal-dependent hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3774
Polymers37,2602
Non-polymers1172
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.477, 71.470, 123.256
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11CHAIN A AND (RESID 3:152)
21CHAIN B AND (RESID 3:152)
31CHAIN C AND (RESID 3:152)
41CHAIN D AND (RESID 3:152)

NCS domain segments:
Dom-IDComponent-IDEns-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111AA3 - 1523 - 152
211BB3 - 1523 - 152
311CC3 - 1523 - 152
411DD3 - 1523 - 152

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Components

#1: Protein
Putative metal-dependent hydrolase


Mass: 18629.930 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: D0VX25*PLUS
#2: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.02 Å3/Da / Density % sol: 39.22 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.0 M Sodium acetate, 0.1 M Imidazole pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97928 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 11, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97928 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. obs: 36943 / % possible obs: 94.2 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.088 / Χ2: 3.112 / Net I/σ(I): 31.776
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.5-2.595.40.28916311.21278.1
2.59-2.695.90.27817271.30582.9
2.69-2.826.20.23318261.49487.7
2.82-2.966.50.21419801.52393.9
2.96-3.1570.18220691.70399.2
3.15-3.397.30.12521122.103100
3.39-3.737.30.09621072.765100
3.73-4.277.30.07521373.366100
4.27-5.387.20.06521554.498100
5.38-406.80.06722608.85299.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.511→35.623 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.35 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: The Friedel pairs were used in phasing.
RfactorNum. reflection% reflection
Rfree0.247 1887 5.11 %
Rwork0.186 --
obs0.189 36943 92.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.915 Å2 / ksol: 0.342 e/Å3
Displacement parametersBiso max: 384.3 Å2 / Biso mean: 68.196 Å2 / Biso min: 19.61 Å2
Baniso -1Baniso -2Baniso -3
1--5.047 Å20 Å2-0 Å2
2--8.919 Å20 Å2
3----3.872 Å2
Refinement stepCycle: LAST / Resolution: 2.511→35.623 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5071 0 4 58 5133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075199
X-RAY DIFFRACTIONf_angle_d0.9087014
X-RAY DIFFRACTIONf_chiral_restr0.081762
X-RAY DIFFRACTIONf_plane_restr0.004893
X-RAY DIFFRACTIONf_dihedral_angle_d16.9781888
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1234X-RAY DIFFRACTIONPOSITIONAL
12B1234X-RAY DIFFRACTIONPOSITIONAL0.043
13C1234X-RAY DIFFRACTIONPOSITIONAL0.039
14D1234X-RAY DIFFRACTIONPOSITIONAL0.041
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.511-2.5790.3821130.2652036214971
2.579-2.6550.2891250.2542283240878
2.655-2.7410.3311300.242385251582
2.741-2.8390.3241550.2262460261586
2.839-2.9530.291410.2392693283492
2.953-3.0870.2981410.2132871301297
3.087-3.2490.2431560.2128893045100
3.249-3.4530.2511750.19228743049100
3.453-3.7190.2351560.18129023058100
3.719-4.0930.2061820.15828963078100
4.093-4.6840.2291480.14329133061100
4.684-5.8970.2031310.14729303061100
5.897-35.6230.1851340.16829243058100
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)
13.26650.39252.51031.8771.14151.4519-0.224-1.04530.17230.0366-0.15180.0701-0.2617-0.52280.22470.15390.1208-0.08610.477-0.161-0.04361.021867.430576.0942
23.63461.62971.2151.17540.39472.08330.2161-0.7039-1.0450.1103-0.0898-0.4118-0.04270.0722-0.08280.09770.0057-0.00540.36450.18090.30755.84546.524770.2372
35.23370.33281.0781.4696-0.3944-0.2096-0.12771.28680.5636-0.33870.16240.18980.0612-0.092-0.0030.1064-0.0378-0.01520.38580.13020.0923-7.261713.642739.1621
42.64610.52530.3311.4562-0.22570.3679-0.17720.50630.0248-0.16010.0778-0.0937-0.03270.33040.08180.2217-0.0103-0.01210.39050.04590.138514.459113.310545.1144
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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