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- PDB-2hcf: Crystal structure of hydrolase haloacid dehalogenase-like family ... -

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Basic information

Entry
Database: PDB / ID: 2hcf
TitleCrystal structure of hydrolase haloacid dehalogenase-like family (np_662590.1) from Chlorobium tepidum TLS at 1.80 A resolution
ComponentsHydrolase, haloacid dehalogenase-like family
KeywordsHYDROLASE / np_662590.1 / hydrolase haloacid dehalogenase-like family / Structural Genomics / PSI-2 / Protein Structure Initiative / Joint Center for Structural Genomics / JCSG
Function / homology
Function and homology information


hydrolase activity / metal ion binding
Similarity search - Function
Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle ...Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Hydrolase, haloacid dehalogenase-like family
Similarity search - Component
Biological speciesChlorobaculum tepidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hydrolase haloacid dehalogenase-like family (np_662590.1) from Chlorobium tepidum TLS at 1.80 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 16, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_asym_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_asym_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.pdbx_leaving_atom_flag / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hydrolase, haloacid dehalogenase-like family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2794
Polymers26,1951
Non-polymers843
Water4,234235
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.750, 71.590, 83.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hydrolase, haloacid dehalogenase-like family /


Mass: 26194.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorobaculum tepidum (bacteria) / Gene: np_662590.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8KBS5
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.01 Å3/Da / Density % sol: 38.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 8.5
Details: 0.2M MgCl2, 30.0% PEG-4000, 0.1M TRIS, pH 8.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837, 0.97915, 0.97929
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 5, 2006 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979151
30.979291
ReflectionResolution: 1.8→27.951 Å / Num. obs: 21098 / % possible obs: 92.2 % / Biso Wilson estimate: 25.562 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 8.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique all% possible all
1.8-1.860.4771.64474271872.7
1.86-1.940.332.36935365484.3
1.94-2.030.2662.76966355185.8
2.03-2.130.2013.86877354193.4
2.13-2.270.1325.37917407796.8
2.27-2.440.1066.57383381897.7
2.44-2.690.0937.37784403897.2
2.69-3.070.0669.37430381096.6
3.070.04414.47814401598.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
REFMAC5.2.0005refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.8→27.951 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.918 / SU B: 6.882 / SU ML: 0.11 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.144
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. MG MODELED IN THE ACTIVE SITE BASED ON CRYSTALLIZATION CONDITIONS AND RELATED STRUCTURES. 4. MG MODELED NEAR GLU 63 BASED ON GEOMETRY AND CRYSTLLIZATION CONDITIONS. 5. CHLORINE MODELED BASED ON CRYSTALLIZATION CONDITIONS. 6. RESIDUES 40-42 WERE DISORDERED AND NOT MODELED. 7. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1084 5.1 %RANDOM
Rwork0.189 ---
obs0.192 21060 97.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.764 Å2
Baniso -1Baniso -2Baniso -3
1-2.23 Å20 Å20 Å2
2---0.52 Å20 Å2
3----1.7 Å2
Refinement stepCycle: LAST / Resolution: 1.8→27.951 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1744 0 3 235 1982
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221783
X-RAY DIFFRACTIONr_bond_other_d0.0010.021679
X-RAY DIFFRACTIONr_angle_refined_deg1.3661.9762408
X-RAY DIFFRACTIONr_angle_other_deg0.833872
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1395227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.06423.29485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.98915315
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1471518
X-RAY DIFFRACTIONr_chiral_restr0.0760.2279
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022001
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02377
X-RAY DIFFRACTIONr_nbd_refined0.2110.2379
X-RAY DIFFRACTIONr_nbd_other0.1810.21718
X-RAY DIFFRACTIONr_nbtor_refined0.1760.2883
X-RAY DIFFRACTIONr_nbtor_other0.0840.21044
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2154
X-RAY DIFFRACTIONr_metal_ion_refined0.0460.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.080.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2440.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.217
X-RAY DIFFRACTIONr_mcbond_it0.9551.51230
X-RAY DIFFRACTIONr_mcbond_other0.211.5465
X-RAY DIFFRACTIONr_mcangle_it1.26821789
X-RAY DIFFRACTIONr_scbond_it2.2313704
X-RAY DIFFRACTIONr_scangle_it3.1954.5617
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 57 -
Rwork0.297 1201 -
obs-1258 82.28 %
Refinement TLS params.Method: refined / Origin x: 22.239 Å / Origin y: 44.9764 Å / Origin z: 15.7082 Å
111213212223313233
T-0.0707 Å20.0126 Å20.007 Å2--0.0257 Å2-0.0012 Å2---0.0338 Å2
L0.4396 °20.0601 °2-0.021 °2-0.8482 °20.1049 °2--1.1383 °2
S0.0059 Å °-0.0257 Å °0.0104 Å °-0.0382 Å °-0.0041 Å °-0.0069 Å °-0.0322 Å °-0.0215 Å °-0.0018 Å °
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Refine TLS-ID: 1 / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDAuth seq-IDLabel seq-ID
12 - 393 - 40
243 - 22944 - 230

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