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- PDB-3pgv: Crystal structure of a haloacid dehalogenase-like hydrolase (KPN_... -

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Entry
Database: PDB / ID: 3pgv
TitleCrystal structure of a haloacid dehalogenase-like hydrolase (KPN_04322) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 2.39 A resolution
Componentshaloacid dehalogenase-like hydrolase
KeywordsHYDROLASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homology
Function and homology information


phosphatase activity / magnesium ion binding
Similarity search - Function
Hypothetical cof family signature 1. / Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 - #10 / Cof family / Hypothetical cof family signature 2. / Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 / HAD-superfamily hydrolase, subfamily IIB / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily ...Hypothetical cof family signature 1. / Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 - #10 / Cof family / Hypothetical cof family signature 2. / Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 / HAD-superfamily hydrolase, subfamily IIB / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Conserved protein, phosphatase-like domain
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.39 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a haloacid dehalogenase-like hydrolase (KPN_04322) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 2.39 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Feb 1, 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: haloacid dehalogenase-like hydrolase
B: haloacid dehalogenase-like hydrolase
C: haloacid dehalogenase-like hydrolase
D: haloacid dehalogenase-like hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,59334
Polymers131,9944
Non-polymers2,59930
Water7,710428
1
A: haloacid dehalogenase-like hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6799
Polymers32,9981
Non-polymers6818
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: haloacid dehalogenase-like hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4936
Polymers32,9981
Non-polymers4955
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: haloacid dehalogenase-like hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4936
Polymers32,9981
Non-polymers4955
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: haloacid dehalogenase-like hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,92813
Polymers32,9981
Non-polymers92912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.569, 61.961, 169.407
Angle α, β, γ (deg.)90.000, 94.190, 90.000
Int Tables number5
Space group name H-MC121
DetailsCRYSTAL PACKING SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE POSSIBLE OLIGOMERIZATION STATE IN SOLUTION.

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
haloacid dehalogenase-like hydrolase / Conserved protein / phosphatase-like domain


Mass: 32998.426 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria)
Strain: MGH 78578 / Gene: yigL, KPN78578_42660, KPN_04322 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6TGK6

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Non-polymers , 5 types, 458 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 428 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE CONSTRUCT (RESIDUES 1-266) WAS EXPRESSED WITH AND CONTAINS A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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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: 2.35 Å3/Da / Density % sol: 47.68 %
Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R-SYM, COMPLETENESS AND
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 15.0% Glycerol, 8.50% iso-Propanol, 17.0% PEG-4000, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97849
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 10, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97849 Å / Relative weight: 1
ReflectionResolution: 2.39→46.778 Å / Num. obs: 48581 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 39.559 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 8.04
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.39-2.480.5381.811710508499.6
2.48-2.570.5372.515791438599.7
2.57-2.690.4763.323560499499.9
2.69-2.830.377422737478499.8
2.83-3.010.2525.723951495299.8
3.01-3.240.197.223242481199.6
3.24-3.570.12110.123832492299.4
3.57-4.080.07913.423385481499.1
4.08-5.120.06315.823509485198.6
5.120.07116.423896497496.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
SHELXphasing
BUSTER-TNTBUSTER 2.8.0refinement
XSCALEdata processing
PDB_EXTRACT3.1data extraction
XDSdata reduction
XSCALEdata scaling
SHELXDphasing
autoSHARPphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: SAD / Resolution: 2.39→46.778 Å / Cor.coef. Fo:Fc: 0.9396 / Cor.coef. Fo:Fc free: 0.9067 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1.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 ...Details: 1.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. 2.PROTEIN ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.3.4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID (EPE), GLYCEROL (GOL), AND 1,2 ETHANEDIOL (EDO) FROM THE CRYSTALLIZATION AND CRYOGENIC CONDITIONS HAVE BEEN MODELED INTO THE STRUCTURE. 4.A METAL ION WITHIN COORDINATION DISTANCE OF THE SIDECHAINS OF ASP 8, ASP 214, THE CARBONYL OXYGEN OF ASP 10, AND OXYGEN ATOMS OF GLYCEROL, AND 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID. IN SOME RELATED STRUCTURES, THIS METAL ION IS MODELED AS CALCIUM, AND IN OTHER RELATED STRUCTURES, IT IS MODELED AS MAGNESIUM. HERE THE METAL ION IS MODELD AS CALCIUM BASED ON A BETTER FIT TO ELECTRON DENSITY MAPS THAN THAT FOR MAGNESIUM. 5. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION. 6. THE REFINEMENT WAS RESTRAINED AGAINST THE SAD PHASES.
RfactorNum. reflection% reflectionSelection details
Rfree0.2106 2450 5.04 %RANDOM
Rwork0.1666 ---
obs0.1688 48579 --
Displacement parametersBiso max: 123.75 Å2 / Biso mean: 43.2808 Å2 / Biso min: 16.27 Å2
Baniso -1Baniso -2Baniso -3
1-8.6179 Å20 Å20.9699 Å2
2---11.1832 Å20 Å2
3---2.5653 Å2
Refinement stepCycle: LAST / Resolution: 2.39→46.778 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8111 0 156 428 8695
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3029SINUSOIDAL8
X-RAY DIFFRACTIONt_trig_c_planes224HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1244HARMONIC5
X-RAY DIFFRACTIONt_it8491HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1063SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10001SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8491HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg11463HARMONIC60.57
X-RAY DIFFRACTIONt_omega_torsion4.12
X-RAY DIFFRACTIONt_other_torsion14.18
LS refinement shellResolution: 2.39→2.45 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2573 205 5.81 %
Rwork0.2133 3324 -
all0.2158 3529 -
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)
12.57080.95890.55761.5798-0.06170.95120.0299-0.0908-0.35370.05-0.0226-0.035-0.03160.0601-0.0073-0.1964-0.03520.0230.03710.0565-0.1007-13.155245.431320.02
22.5983-0.4763-0.31650.38730.02861.603-0.0215-0.08450.13420.04220.0629-0.0619-0.023-0.0168-0.0414-0.07480.0799-0.0019-0.02240.0075-0.1067-31.498250.760162.5212
34.71621.8777-0.32451.615-0.42240.8790.1942-0.5152-0.26020.0943-0.2502-0.1482-0.03980.01990.056-0.2425-0.0764-0.0220.02260.0008-0.1783-42.30431.192719.1177
41.7325-1.1648-0.40641.30380.47071.08480.01310.09110.18540.02850-0.1440.01760.0401-0.0131-0.14450.0602-0.01090.08160.0057-0.1183-1.015434.64361.0768
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|*}A2 - 265
2X-RAY DIFFRACTION2{B|*}B1 - 266
3X-RAY DIFFRACTION3{C|*}C1 - 266
4X-RAY DIFFRACTION4{D|*}D1 - 266

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