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- PDB-3dl1: Crystal structure of a Putative Metal-dependent Hydrolase (YP_001... -

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Basic information

Entry
Database: PDB / ID: 3dl1
TitleCrystal structure of a Putative Metal-dependent Hydrolase (YP_001336084.1) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 2.20 A resolution
ComponentsPutative Metal-dependent Hydrolase
KeywordsHYDROLASE / YP_001336084.1 / A Putative Metal-dependent Hydrolase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Protein of unknown function (DUF980) / unknown function
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: 2.2 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
DepositionJun 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 23, 2012Group: Database references
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jul 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 1.5Feb 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)30,7092
Polymers30,6741
Non-polymers351
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)131.050, 131.050, 37.150
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)
Gene: YP_001336084.1, mtfA, KPN78578_23930, KPN_02432 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6TB83
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / 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. THE TARGET PROTEIN SEQUENCE MATCHES TO GENBANK ENTRY YP_001336084.1.YP_001336084.1, COMPARED TO UNP MATCH A6TB83, HAS AN EXTRA RESIDEU MET AT THE BEGINNING OF THE 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: 52.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1.0000M (NH4)2HPO4, 0.2000M NaCl, 0.1M Imidazole pH 8.0, 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
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 16, 2008 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.2→29.311 Å / Num. obs: 17061 / % possible obs: 99.9 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 5.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.2-2.267.30.6781.1884112120.678100
2.26-2.327.30.4581.6896512300.458100
2.32-2.397.20.4131.8834511520.413100
2.39-2.467.40.3222.3836611330.322100
2.46-2.547.20.292.6795411040.29100
2.54-2.637.30.2213.4792110790.221100
2.63-2.737.20.1863.9743910350.186100
2.73-2.847.30.1415.2742810140.141100
2.84-2.977.20.1186.168029480.118100
2.97-3.117.30.0977.267689310.097100
3.11-3.287.20.0897.561928650.089100
3.28-3.487.20.0788.359568330.078100
3.48-3.727.10.0738.556998020.073100
3.72-4.0270.0718.551797400.071100
4.02-4.470.0581047836870.058100
4.4-4.926.90.05311.343196220.053100
4.92-5.686.80.0579.938555680.057100
5.68-6.966.50.0649.531474820.064100
6.96-9.846.30.0521125033950.052100
9.84-29.315.30.04713.312202290.04795.2

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3.004data extraction
MOSFLMdata reduction
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→29.311 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.959 / SU B: 8.619 / SU ML: 0.109 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.15
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.202 861 5.1 %RANDOM
Rwork0.171 ---
obs0.172 16997 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.533 Å2
Baniso -1Baniso -2Baniso -3
1-1.14 Å20 Å20 Å2
2--1.14 Å20 Å2
3----2.29 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.311 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1664 0 1 97 1762
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221731
X-RAY DIFFRACTIONr_bond_other_d0.0010.021147
X-RAY DIFFRACTIONr_angle_refined_deg1.3751.9462366
X-RAY DIFFRACTIONr_angle_other_deg0.92832787
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9835213
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.30323.57184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.2215263
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.881511
X-RAY DIFFRACTIONr_chiral_restr0.0890.2262
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021936
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02366
X-RAY DIFFRACTIONr_nbd_refined0.2090.2337
X-RAY DIFFRACTIONr_nbd_other0.1830.21146
X-RAY DIFFRACTIONr_nbtor_refined0.1780.2825
X-RAY DIFFRACTIONr_nbtor_other0.0870.2852
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.267
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3350.215
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0790.25
X-RAY DIFFRACTIONr_mcbond_it2.14431154
X-RAY DIFFRACTIONr_mcbond_other0.4643416
X-RAY DIFFRACTIONr_mcangle_it3.21551704
X-RAY DIFFRACTIONr_scbond_it5.5668737
X-RAY DIFFRACTIONr_scangle_it7.31511659
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 61 -
Rwork0.241 1144 -
all-1205 -
obs--99.34 %
Refinement TLS params.Method: refined / Origin x: 50.6167 Å / Origin y: 23.6789 Å / Origin z: 8.5781 Å
111213212223313233
T-0.0905 Å20.0668 Å20.0467 Å2--0.0374 Å20.0732 Å2---0.116 Å2
L2.549 °20.4932 °20.1559 °2-1.4419 °20.1114 °2--1.4342 °2
S0.0746 Å °-0.2828 Å °-0.2943 Å °-0.0665 Å °-0.0556 Å °-0.0929 Å °0.0447 Å °0.1371 Å °-0.0189 Å °

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