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- PDB-4ovy: Crystal structure of Haloacid dehalogenase domain protein hydrola... -

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Basic information

Entry
Database: PDB / ID: 4ovy
TitleCrystal structure of Haloacid dehalogenase domain protein hydrolase from Planctomyces limnophilus DSM 3776
ComponentsHaloacid dehalogenase domain protein hydrolase
KeywordsHYDROLASE / putative phosphatase / MCSG / PSI-biology / Structural Genomics / Midwest Center for Structural Genomics
Function / homologyhaloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / hydrolase activity / metal ion binding / CITRIC ACID / Haloacid dehalogenase domain protein hydrolase
Function and homology information
Biological speciesPlanctomyces limnophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsChang, C. / Gu, M. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be published
Title: Crystal structure of Haloacid dehalogenase domain protein hydrolase from Planctomyces limnophilus DSM 3776
Authors: Chang, C. / Gu, M. / Endres, M. / Joachimiak, A.
History
DepositionJan 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Derived calculations
Revision 1.2Nov 22, 2017Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_validate_close_contact / software / struct_site
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _struct_site.details
Revision 1.3Dec 27, 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 / refine_hist / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Haloacid dehalogenase domain protein hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,53310
Polymers35,7361
Non-polymers7979
Water4,252236
1
A: Haloacid dehalogenase domain protein hydrolase
hetero molecules

A: Haloacid dehalogenase domain protein hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,06620
Polymers71,4732
Non-polymers1,59318
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area5880 Å2
ΔGint1 kcal/mol
Surface area25680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.950, 75.502, 64.357
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-535-

HOH

21A-572-

HOH

31A-575-

HOH

41A-579-

HOH

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Components

#1: Protein Haloacid dehalogenase domain protein hydrolase


Mass: 35736.480 Da / Num. of mol.: 1 / Fragment: UNP residues 24-333
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Planctomyces limnophilus (bacteria) / Strain: DSM 3776 / Gene: Plim_1241 / Plasmid: pMCSG73 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pGrow7-K / References: UniProt: D5SUM3
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.51 Å3/Da / Density % sol: 50.92 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.8 M Tris-Ammonium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97899 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 16, 2012
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97899 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 33799 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Rmerge(I) obs: 0.077 / Χ2: 0.907 / Net I/av σ(I): 24.677 / Net I/σ(I): 10 / Num. measured all: 192032
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.8-1.835.10.94716570.83999.9
1.83-1.865.30.88216690.887100
1.86-1.95.50.76716610.893100
1.9-1.945.70.63416580.882100
1.94-1.985.80.54416840.905100
1.98-2.035.80.43516680.885100
2.03-2.085.80.34816650.906100
2.08-2.135.80.28916560.93100
2.13-2.25.80.24616600.946100
2.2-2.275.80.20416900.906100
2.27-2.355.80.17116760.895100
2.35-2.445.80.1416840.865100
2.44-2.555.80.11816770.855100
2.55-2.695.80.10117010.88100
2.69-2.865.80.07816900.907100
2.86-3.085.80.0616920.89799.9
3.08-3.395.70.04717140.918100
3.39-3.885.60.03517120.86299.9
3.88-4.885.70.03117530.81899.9
4.88-505.40.04518321.25599

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.8→29.62 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.18 / SU ML: 0.059 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.102
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1746 1551 5 %RANDOM
Rwork0.1309 29183 --
obs0.1332 30734 90.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 84.73 Å2 / Biso mean: 27.062 Å2 / Biso min: 15.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2---1.72 Å2-0 Å2
3---1.79 Å2
Refinement stepCycle: final / Resolution: 1.8→29.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2446 0 51 236 2733
Biso mean--47.18 37.37 -
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0192596
X-RAY DIFFRACTIONr_bond_other_d0.0010.022473
X-RAY DIFFRACTIONr_angle_refined_deg1.1031.9813518
X-RAY DIFFRACTIONr_angle_other_deg0.72335687
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2435313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.81922.869122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.38115407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.1831525
X-RAY DIFFRACTIONr_chiral_restr0.0660.2375
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212914
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02601
X-RAY DIFFRACTIONr_rigid_bond_restr1.49735069
X-RAY DIFFRACTIONr_sphericity_free30.554586
X-RAY DIFFRACTIONr_sphericity_bonded10.65355161
LS refinement shellResolution: 1.796→1.843 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.21 66 -
Rwork0.159 1219 -
all-1285 -
obs--51.84 %

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