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- PDB-3kl7: Crystal structure of Putative metal-dependent hydrolase (YP_00130... -

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Basic information

Entry
Database: PDB / ID: 3kl7
TitleCrystal structure of Putative metal-dependent hydrolase (YP_001302908.1) from Parabacteroides distasonis ATCC 8503 at 2.30 A resolution
ComponentsPutative metal-dependent hydrolase
KeywordsHYDROLASE / Putative metal-dependent 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
Beta-lactamase superfamily domain / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Unknown ligand / Putative metal-dependent hydrolase
Similarity search - Component
Biological speciesParabacteroides distasonis ATCC 8503 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative metal-dependent hydrolase (YP_001302908.1) from Parabacteroides distasonis ATCC 8503 at 2.30 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: pdbx_struct_conn_angle / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative metal-dependent hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5289
Polymers26,9691
Non-polymers5588
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.034, 95.034, 63.295
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Putative metal-dependent hydrolase


Mass: 26969.473 Da / Num. of mol.: 1 / Fragment: sequence database residues 26-241
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides distasonis ATCC 8503 (bacteria)
Strain: ATCC 8503 / DSM 20701 / NCTC 11152 / Gene: BDI_1531 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6LC72

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Non-polymers , 5 types, 163 molecules

#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHIS CONSTRUCT (26-241) WAS EXPRESSED WITH THE N-TERMINAL 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: 3.06 Å3/Da / Density % sol: 59.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 38.0000% polyethylene glycol 300, 0.2500M calcium acetate, 0.1M sodium cacodylate pH 7.0, NANODROP, 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: 0.9792
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 15, 2009 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.3→29.54 Å / Num. obs: 14896 / % possible obs: 99.6 % / Redundancy: 7.4 % / Biso Wilson estimate: 32.531 Å2 / Rmerge(I) obs: 0.22 / Rsym value: 0.22 / Net I/σ(I): 10.2
Reflection shell

Rmerge(I) obs: 0.013 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.3-2.367.41.8821111031.25299
2.36-2.427.52.2791710611.05799.7
2.42-2.497.52.3763810220.96899.4
2.49-2.577.42.772939790.82599.4
2.57-2.667.43.372819840.68499.4
2.66-2.757.43.868349240.58899.5
2.75-2.857.54.268869220.53299.9
2.85-2.977.45.464428680.40299.6
2.97-3.17.57.162888430.32799.5
3.1-3.257.48.858817960.25799.7
3.25-3.437.411.657767830.19199.8
3.43-3.647.415.553137220.14299.8
3.64-3.897.318.450146840.11899.8
3.89-4.27.321.447756570.09999.8
4.2-4.67.325.842395830.08299.8
4.6-5.147.227.339945510.07499.9
5.14-5.947.122.234594850.09599.9
5.94-7.277.121.829024100.10399.9
7.27-10.296.83122753340.06999.9
10.29-29.546.337.511601850.05695.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→29.54 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 11.04 / SU ML: 0.122 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.212 / ESU R Free: 0.177
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE 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 THE 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. TWO ZINC IONS HAVE BEEN MODELED AT THE PUTATIVE ACTIVE SITE BASED ON AN X-RAY FLUORESCENCE EXCITATION SCAN SPECTRUM AND ANOMALOUS DIFFERENCE FOURIER PEAKS. 5. AN UNIDENTIFIED LIGAND (UNL) HAS BEEN MODELED AT THE PUTATIVE ACTIVE SITE COORDINATING THE ZINC SITES. 6. ACETATE (ACT) AND GLYCEROL (GOL) FROM THE CRYSTALLIZATION/ CRYOPROTECTANT SOLUTIONS HAVE BEEN MODELED INTO THE SOLVENT STRUCTURE. 7. TLS GROUPS WERE ASSIGNED WITH THE AID OF THE TLSMD SERVER.
RfactorNum. reflection% reflectionSelection details
Rfree0.204 750 5 %RANDOM
Rwork0.164 ---
obs0.166 14894 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 55.96 Å2 / Biso mean: 17.881 Å2 / Biso min: 4.15 Å2
Baniso -1Baniso -2Baniso -3
1-1.9 Å20.95 Å20 Å2
2--1.9 Å20 Å2
3----2.85 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1734 0 36 155 1925
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221817
X-RAY DIFFRACTIONr_bond_other_d0.0020.021241
X-RAY DIFFRACTIONr_angle_refined_deg1.0591.9782456
X-RAY DIFFRACTIONr_angle_other_deg0.70933047
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0425225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.98624.81983
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.9215319
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.167158
X-RAY DIFFRACTIONr_chiral_restr0.0910.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211998
X-RAY DIFFRACTIONr_gen_planes_other00.02342
X-RAY DIFFRACTIONr_mcbond_it0.46121109
X-RAY DIFFRACTIONr_mcbond_other0.092445
X-RAY DIFFRACTIONr_mcangle_it0.87631801
X-RAY DIFFRACTIONr_scbond_it1.3154708
X-RAY DIFFRACTIONr_scangle_it1.9635652
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 66 -
Rwork0.252 1019 -
all-1085 -
obs--98.55 %
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)
18.6982.16940.59731.8345-0.16793.5592-0.0265-0.2704-0.48240.05260.031-0.04870.4123-0.0563-0.00450.14610.00810.01150.0412-0.01540.082258.20617.4799.255
21.61460.23560.37741.39360.12982.7523-0.02570.11460.03440.00430.0055-0.07010.04290.09940.02020.0041-0.00160.0060.03140.01110.053764.32728.725.708
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 46
2X-RAY DIFFRACTION2A47 - 241

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