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- PDB-2pke: Crystal structure of haloacid delahogenase-like family hydrolase ... -

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Basic information

Entry
Database: PDB / ID: 2pke
TitleCrystal structure of haloacid delahogenase-like family hydrolase (NP_639141.1) from Xanthomonas campestris at 1.81 A resolution
ComponentsHaloacid delahogenase-like family hydrolase
KeywordsHYDROLASE / NP_639141.1 / haloacid delahogenase-like family hydrolase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


hydrolase activity / metal ion binding
Similarity search - Function
: / Haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD superfamily/HAD-like / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold ...: / Haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD superfamily/HAD-like / haloacid dehalogenase-like hydrolase / 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
DI(HYDROXYETHYL)ETHER / Hydrolase, haloacid delahogenase-like family
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.81 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of haloacid delahogenase-like family hydrolase (NP_639141.1) from Xanthomonas campestris at 1.81 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2007Provider: 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 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Jan 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.conn_type_id / _struct_conn.id / _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_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
Revision 1.6Oct 30, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999 SEQUENCE 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: Haloacid delahogenase-like family hydrolase
B: Haloacid delahogenase-like family hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3438
Polymers56,0812
Non-polymers2616
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-68 kcal/mol
Surface area19760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.160, 107.100, 62.560
Angle α, β, γ (deg.)90.000, 102.290, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B

NCS domain segments:

Component-ID: 1 / Refine code: 6

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYASPASPAA9 - 4610 - 47
21GLYGLYASPASPBB9 - 4610 - 47
12PHEPHETYRTYRAA67 - 20768 - 208
22PHEPHETYRTYRBB67 - 20768 - 208
13ASPASPGLNGLNAA222 - 249223 - 250
23ASPASPGLNGLNBB222 - 249223 - 250

NCS ensembles :
ID
1
2
3
DetailsSIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Haloacid delahogenase-like family hydrolase


Mass: 28040.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria)
Species: Xanthomonas campestris / Strain: NCPPB 528, LMG 568 / Gene: NP_639141.1, XCC3796 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8P4B4
#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


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O
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: 1.99 Å3/Da / Density % sol: 38.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: NANODROP, 0.2M MgCl2, 20.0% PEG 8000, 0.1M Tris-HCl pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162, 0.97936
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 1, 2007 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979361
ReflectionResolution: 1.81→29.386 Å / Num. obs: 37341 / % possible obs: 82.4 % / Biso Wilson estimate: 29.733 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 7.74
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique all% possible all
1.81-1.870.351.61072337845.9
1.87-1.950.32522132478856.6
1.95-2.040.272.63968637379.7
2.04-2.150.2273.14646699786.3
2.15-2.280.17444457673188.3
2.28-2.460.13554877731891.3
2.46-2.70.1056.24682707992.2
2.7-3.090.0659.34929743293.5
3.090.03415.44910746594.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0019refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.81→29.386 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / SU B: 7.243 / SU ML: 0.11 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.147 / ESU R Free: 0.142
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. THE SIDE CHAIN OF THE RESIDUES 46-52, 208-222 IN THE A SUBUNIT AND 60-67, 207-216 IN THE B SUBUNIT WERE DISORDERED AND WERE NOT MODELED. 5. RAMACHANDRAN OUTLIER OF RESIDUE ARG 51 IN SUBUNIT A IS LOCATED IN POOR DENSITY. 6. MAGNESIUM (MG) AND CL IONS FROM THE CRYSTALLIZATION BUFFER WERE MODELED INTO THE STRUCTURE. 7. PEG8000 FRAGMENTS (PEG) FROM CRYSTALLIZATION SOLUTION ARE MODELLED.
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1871 5 %RANDOM
Rwork0.178 ---
all0.181 ---
obs0.181 37314 93.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.525 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20 Å2-0.14 Å2
2--0.91 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.81→29.386 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3524 0 12 255 3791
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223654
X-RAY DIFFRACTIONr_bond_other_d0.0020.022438
X-RAY DIFFRACTIONr_angle_refined_deg1.5961.9654967
X-RAY DIFFRACTIONr_angle_other_deg0.99435936
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4845467
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.07124.26169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.04515589
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2831527
X-RAY DIFFRACTIONr_chiral_restr0.0940.2557
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024154
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02731
X-RAY DIFFRACTIONr_nbd_refined0.2160.2815
X-RAY DIFFRACTIONr_nbd_other0.2020.22560
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21805
X-RAY DIFFRACTIONr_nbtor_other0.0870.21893
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2226
X-RAY DIFFRACTIONr_metal_ion_refined0.0290.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2780.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2890.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2220.215
X-RAY DIFFRACTIONr_mcbond_it2.23432376
X-RAY DIFFRACTIONr_mcbond_other0.6283948
X-RAY DIFFRACTIONr_mcangle_it3.28753716
X-RAY DIFFRACTIONr_scbond_it5.4481449
X-RAY DIFFRACTIONr_scangle_it8.141111251
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1460LOOSE POSITIONAL0.315
1460LOOSE THERMAL3.3310
21750LOOSE POSITIONAL0.675
21750LOOSE THERMAL2.8210
3345LOOSE POSITIONAL0.525
3345LOOSE THERMAL4.0510
LS refinement shellResolution: 1.81→1.857 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 109 -
Rwork0.263 1824 -
obs-1933 66.04 %
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)
10.6842-0.16130.31560.6327-0.74331.53710.02280.0255-0.0627-0.0825-0.04370.01690.11650.04770.0209-0.0584-0.00010.0046-0.0383-0.0186-0.034-4.207324.400454.1637
20.64320.0637-0.00961.34010.43540.66370.0324-0.1023-0.01840.0337-0.0666-0.0185-0.0017-0.01870.0342-0.0616-0.0012-0.006-0.02240.0236-0.0666-3.084931.26180.8451
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA0 - 2501 - 251
22BB9 - 24910 - 250

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