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- PDB-3dto: Crystal structure of the metal-dependent HD domain-containing hyd... -

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Basic information

Entry
Database: PDB / ID: 3dto
TitleCrystal structure of the metal-dependent HD domain-containing hydrolase BH2835 from Bacillus halodurans, Northeast Structural Genomics Consortium Target BhR130.
ComponentsBH2835 protein
Keywordsstructural genomics / unknown function / all alpha-helical protein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


HD-domain/PDEase-like / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1910 / HD domain / HD domain / Cyclin A; domain 1 / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.3 Å
AuthorsForouhar, F. / Su, M. / Seetharaman, J. / Janjua, H. / Fang, Y. / Xiao, R. / Cunningham, K. / Ma, L.-C. / Owen, L.A. / Wang, D. ...Forouhar, F. / Su, M. / Seetharaman, J. / Janjua, H. / Fang, Y. / Xiao, R. / Cunningham, K. / Ma, L.-C. / Owen, L.A. / Wang, D. / Tong, S. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the metal-dependent HD domain-containing hydrolase BH2835 from Bacillus halodurans, Northeast Structural Genomics Consortium Target BhR130.
Authors: Forouhar, F. / Su, M. / Seetharaman, J. / Janjua, H. / Fang, Y. / Xiao, R. / Cunningham, K. / Ma, L.-C. / Owen, L.A. / Wang, D. / Tong, S. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionJul 15, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BH2835 protein
B: BH2835 protein
C: BH2835 protein
D: BH2835 protein


Theoretical massNumber of molelcules
Total (without water)104,8164
Polymers104,8164
Non-polymers00
Water00
1
A: BH2835 protein
B: BH2835 protein


Theoretical massNumber of molelcules
Total (without water)52,4082
Polymers52,4082
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-19 kcal/mol
Surface area20210 Å2
MethodPISA
2
C: BH2835 protein
D: BH2835 protein


Theoretical massNumber of molelcules
Total (without water)52,4082
Polymers52,4082
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-19 kcal/mol
Surface area20160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.564, 47.987, 111.159
Angle α, β, γ (deg.)90.00, 89.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
BH2835 protein


Mass: 26204.098 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Strain: C-125 / Gene: BH2835 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q9K916
Has protein modificationY

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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: 2.48 Å3/Da / Density % sol: 50.45 %
Crystal growTemperature: 291 K / Method: microbatch under oil / pH: 7
Details: Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, and 5 mM DTT. Reservoir solution: 0.1M mops (pH 7), 80% PEG 400, and 0.1M potassium acetate. , microbatch under oil, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 19, 2007 / Details: mirrors.
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.3→30 Å / Num. obs: 22713 / % possible obs: 74.5 % / Observed criterion σ(F): 0.5 / Observed criterion σ(I): 0.5 / Redundancy: 3.4 % / Biso Wilson estimate: 74.8 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.075 / Net I/σ(I): 13.1
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.149 / Mean I/σ(I) obs: 3 / Rsym value: 0.185 / % possible all: 58.4

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Processing

Software
NameVersionClassification
CNS1.2refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
SnBthen SOLVE/RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 3.3→19.76 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 335033.32 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.292 2147 9.5 %RANDOM
Rwork0.248 ---
obs0.248 22713 76.3 %-
all-15076 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.1144 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 70.3 Å2
Baniso -1Baniso -2Baniso -3
1-21.68 Å20 Å21.82 Å2
2---2.83 Å20 Å2
3----18.85 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.58 Å0.45 Å
Luzzati d res low-5 Å
Luzzati sigma a0.87 Å0.64 Å
Refinement stepCycle: LAST / Resolution: 3.3→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6132 0 0 0 6132
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.3→3.42 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.32 136 10.3 %
Rwork0.286 1190 -
obs--43.4 %

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