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- PDB-2qpx: Crystal structure of putative metal-dependent hydrolase (YP_80573... -

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Basic information

Entry
Database: PDB / ID: 2qpx
TitleCrystal structure of putative metal-dependent hydrolase (YP_805737.1) from Lactobacillus casei ATCC 334 at 1.40 A resolution
ComponentsPredicted metal-dependent hydrolase of the TIM-barrel fold
KeywordsHYDROLASE / YP_805737.1 / putative metal-dependent hydrolase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / UNKNOWN FUNCTION
Function / homology
Function and homology information


hydrolase activity / metal ion binding
Similarity search - Function
Amidohydrolase / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Predicted metal-dependent hydrolase of the TIM-barrel fold
Similarity search - Component
Biological speciesLactobacillus casei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative metal-dependent hydrolase (YP_805737.1) from Lactobacillus casei ATCC 334 at 1.40 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_conn_type / 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 / _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_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_conn_type.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 300 BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION ... BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A TRIMER AS A BIOLOGICALLY 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: Predicted metal-dependent hydrolase of the TIM-barrel fold
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,92914
Polymers43,1161
Non-polymers81413
Water8,863492
1
A: Predicted metal-dependent hydrolase of the TIM-barrel fold
hetero molecules

A: Predicted metal-dependent hydrolase of the TIM-barrel fold
hetero molecules

A: Predicted metal-dependent hydrolase of the TIM-barrel fold
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,78842
Polymers129,3473
Non-polymers2,44139
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area15050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.170, 142.170, 142.170
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-543-

HOH

21A-570-

HOH

31A-611-

HOH

DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A MONOMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Predicted metal-dependent hydrolase of the TIM-barrel fold


Mass: 43115.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus casei (bacteria) / Strain: ATCC 334 / Gene: YP_805737.1, LSEI_0440 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q03BX7
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 492 / 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: 2.78 Å3/Da / Density % sol: 55.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: NANODROP, 1.0M LiCl, 20.0% PEG 6000, 0.1M HEPES pH 7.0, 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: 0.91837, 0.97917, 0.97891
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 1, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979171
30.978911
ReflectionResolution: 1.4→29.025 Å / Num. obs: 93379 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 16.76 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 16.16
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.4-1.450.0111.713367118055198.5
1.45-1.510.0112.2141679188911100
1.51-1.580.0112.9139693185471100
1.58-1.660.0113.9132288174841100
1.66-1.760.0115.5134893177511100
1.76-1.90.0118.4143534188061100
1.9-2.090.01115.1139632182111100
2.09-2.390.01124.5139974181731100
2.39-3.010.01137.1141694183671100
3.01-29.0250.01159.914063418383199.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.4→29.025 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.837 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.049 / ESU R Free: 0.047
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. LYSINE 166 (KCX) IS CABOXYLATED BASED ON INTEPRETATION OF ELECTRON DENSITY, INTERACTIONS AND STRUCTURAL HOMOLOGS. EDO MOLECULES ARE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. LYSINE 166 (KCX) IS CABOXYLATED BASED ON INTEPRETATION OF ELECTRON DENSITY, INTERACTIONS AND STRUCTURAL HOMOLOGS. EDO MOLECULES ARE FROM CRYO CONDITIONS. 3. THERE ARE TWO METAL IONS (ZINC) IN THE ACTIVE SITE. THE PRESENCE OF THE ZINC AT BOTH SITES IS SUPPORTED BY X-RAY FLUORESCENCE MEASUREMENTS, ANOMALOUS DIFFERENCE FOURIERS AND GEOMETRY. THE OCCUPANCIES OF BOTH METAL IONS ARE ADJUSTED TO REFLECT PEAK HEIGHTS IN ANOMALOUS DIFFERENCE MAPS AND 2FO-FC MAP. 4. 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 0.80 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.162 4683 5 %RANDOM
Rwork0.134 ---
obs0.135 93378 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.7 Å2
Refinement stepCycle: LAST / Resolution: 1.4→29.025 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3012 0 46 492 3550
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223334
X-RAY DIFFRACTIONr_bond_other_d0.0020.022272
X-RAY DIFFRACTIONr_angle_refined_deg1.5431.9544547
X-RAY DIFFRACTIONr_angle_other_deg1.01435547
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8835430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.02924.142169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.69215544
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9941517
X-RAY DIFFRACTIONr_chiral_restr0.0980.2483
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023774
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02711
X-RAY DIFFRACTIONr_nbd_refined0.2350.2704
X-RAY DIFFRACTIONr_nbd_other0.1980.22323
X-RAY DIFFRACTIONr_nbtor_refined0.1880.21584
X-RAY DIFFRACTIONr_nbtor_other0.0890.21575
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2345
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0140.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0910.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3270.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2630.216
X-RAY DIFFRACTIONr_mcbond_it2.7932146
X-RAY DIFFRACTIONr_mcbond_other1.9543784
X-RAY DIFFRACTIONr_mcangle_it3.39753198
X-RAY DIFFRACTIONr_scbond_it4.59481505
X-RAY DIFFRACTIONr_scangle_it5.901111323
X-RAY DIFFRACTIONr_rigid_bond_restr2.03336485
X-RAY DIFFRACTIONr_sphericity_free8.8033496
X-RAY DIFFRACTIONr_sphericity_bonded4.86835499
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 362 -
Rwork0.28 6495 -
obs-6857 99.78 %

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