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- PDB-3khi: Crystal structure of a Putative Metal-dependent Hydrolase (YP_001... -

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Basic information

Entry
Database: PDB / ID: 3khi
TitleCrystal structure of a Putative Metal-dependent Hydrolase (YP_001336084.1) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.95 A resolution
ComponentsPutative Metal-dependent Hydrolase
KeywordsHYDROLASE / A Putative Metal-dependent Hydrolase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / aminopeptidase activity / metallopeptidase activity / proteolysis / metal ion binding / cytoplasm
Similarity search - Function
Glucose-regulated metallo-peptidase M90, N-terminal domain / MtfA family / MtfA, N-terminal / Glucose-regulated metallo-peptidase M90 / Cyclin A; domain 1 / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Orthogonal Bundle / 3-Layer(aba) Sandwich ...Glucose-regulated metallo-peptidase M90, N-terminal domain / MtfA family / MtfA, N-terminal / Glucose-regulated metallo-peptidase M90 / Cyclin A; domain 1 / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Mlc titration factor A
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae MGH 78578 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: J.Bacteriol. / Year: 2012
Title: The Structure of Mlc Titration Factor A (MtfA/YeeI) Reveals a Prototypical Zinc Metallopeptidase Related to Anthrax Lethal Factor.
Authors: Xu, Q. / Gohler, A.K. / Kosfeld, A. / Carlton, D. / Chiu, H.J. / Klock, H.E. / Knuth, M.W. / Miller, M.D. / Elsliger, M.A. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Jahreis, K. / Wilson, I.A.
History
DepositionOct 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 23, 2012Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jul 17, 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 1.5Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)31,1209
Polymers30,6741
Non-polymers4478
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)131.190, 131.190, 37.120
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Putative Metal-dependent Hydrolase / Mlc titration factor A


Mass: 30673.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae MGH 78578 (bacteria)
Strain: ATCC 700721 / MGH 78578 / Gene: mtfA, KPN78578_23930, KPN_02432 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6TB83
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 10.0000% polyethylene glycol 6000, 1.0000M lithium chloride, 0.1M Bicine pH 9.0, 0.001 M zinc chloride, 0.001 M Leucine-Chloromethyl ketone, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97951
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 17, 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: 0.97951 Å / Relative weight: 1
ReflectionResolution: 1.95→46.374 Å / Num. obs: 24283 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 36.556 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 14.52
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.95-2.040.9772.1216192992199.8
2.04-2.120.5823.4162702244199.8
2.12-2.220.44.9174392404199.9
2.22-2.340.2796.81714423701100
2.34-2.480.29.21622722411100
2.48-2.670.13512.81675823211100
2.67-2.940.09117.9168422353199.9
2.94-3.360.06324.21689823701100
3.36-4.230.04531.6168672411199.9
4.23-46.3740.04732.9164782577199.4

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→46.374 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.952 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 6.311 / SU ML: 0.081 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.129 / ESU R Free: 0.122
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN 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 RECORDS CONTAIN 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. ZINC (ZN), CHLORIDE (CL) AND 1,2-ETHANEDIOL (EDO) MODELED ARE PRESENT IN CRYSTALLIZATION/CRYO CONDITIONS. 5. ZINC ASSIGNMENT IS BASED ON X-RAY FLUORESCENCE SPECTROSCOPY AND ANOMALOUS DIFFERENCE FOURIER MAPS. 6. THERE ARE SOME UNINTERPRETED DENSITIES NEAR THE PUTATIVE ACTIVE SITE.
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1244 5.1 %RANDOM
Rwork0.183 ---
obs0.184 24240 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 88.17 Å2 / Biso mean: 30.899 Å2 / Biso min: 8.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20 Å2
2--0.15 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.95→46.374 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1737 0 23 123 1883
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221859
X-RAY DIFFRACTIONr_bond_other_d0.0020.021226
X-RAY DIFFRACTIONr_angle_refined_deg1.2761.9432543
X-RAY DIFFRACTIONr_angle_other_deg0.91832994
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1535240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.6524.33390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.09615277
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.485159
X-RAY DIFFRACTIONr_chiral_restr0.0740.2282
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212100
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02380
X-RAY DIFFRACTIONr_mcbond_it1.72831146
X-RAY DIFFRACTIONr_mcbond_other0.393451
X-RAY DIFFRACTIONr_mcangle_it2.9351842
X-RAY DIFFRACTIONr_scbond_it4.8368713
X-RAY DIFFRACTIONr_scangle_it6.73511691
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 84 -
Rwork0.279 1644 -
all-1728 -
obs--99.94 %
Refinement TLS params.Method: refined / Origin x: -14.8738 Å / Origin y: 40.7589 Å / Origin z: 0.955 Å
111213212223313233
T0.0653 Å2-0.0466 Å2-0.0319 Å2-0.0778 Å20.0467 Å2--0.0385 Å2
L2.6535 °20.0748 °2-0.2352 °2-1.6183 °2-0.0516 °2--1.1182 °2
S0.0366 Å °0.2761 Å °0.2083 Å °0.0857 Å °-0.0095 Å °-0.107 Å °-0.0185 Å °0.0374 Å °-0.0271 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 253
2X-RAY DIFFRACTION1A301

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