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- PDB-3ieh: Crystal structure of Putative metallopeptidase (YP_001051774.1) f... -

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Basic information

Entry
Database: PDB / ID: 3ieh
TitleCrystal structure of Putative metallopeptidase (YP_001051774.1) from SHEWANELLA BALTICA OS155 at 2.45 A resolution
ComponentsPutative metallopeptidase
KeywordsHYDROLASE / YP_001051774.1 / Putative metallopeptidase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


hydrolase activity, acting on ester bonds / metallocarboxypeptidase activity / proteolysis / zinc ion binding
Similarity search - Function
AstE/AspA barrel-sandwich hybrid domain / : / Succinylglutamate desuccinylase/Aspartoacylase catalytic domain / Peptidase family M14 domain profile. / Peptidase M14, carboxypeptidase A / Zn peptidases / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Unknown ligand / Peptidase M14 domain-containing protein
Similarity search - Component
Biological speciesShewanella baltica OS155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.45 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative metallopeptidase (YP_001051774.1) from SHEWANELLA BALTICA OS155 at 2.45 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / 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 1.4Feb 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
Revision 1.5Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative metallopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,82114
Polymers30,5841
Non-polymers1,23713
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.958, 80.958, 87.940
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
DetailsCRYSTAL PACKING ANALYSIS AND ANALYTICAL SIZE-EXCLUSION CHROMATOGRAPHY COUPLED WITH STATIC LIGHT SCATTERING SUPPORT THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIC FORM IN SOLUTION.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Putative metallopeptidase


Mass: 30583.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella baltica OS155 (bacteria) / Gene: Sbal_3428, YP_001051774.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A3D842

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Non-polymers , 6 types, 79 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS 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: 2.72 Å3/Da / Density % sol: 54.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 10.0000% Glycerol, 5.0000% PEG-1000, 30.0000% PEG-600, 0.1M MES pH 6.0, Additive: 0.006 M Zinc Chloride, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97845,0.97752,0.91837
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 16, 2009 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978451
20.977521
30.918371
ReflectionResolution: 2.45→29.775 Å / Num. obs: 12080 / % possible obs: 99.8 % / Redundancy: 7.6 % / Biso Wilson estimate: 34.498 Å2 / Rmerge(I) obs: 0.166 / Rsym value: 0.166 / Net I/σ(I): 11.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.45-2.517.60.7572.767428850.75799.8
2.51-2.587.60.6471.265528660.647100
2.58-2.667.60.5521.463798390.55299.9
2.66-2.747.60.51.561838120.599.9
2.74-2.837.60.4241.861048010.42499.9
2.83-2.937.60.3542.158287670.35499.8
2.93-3.047.60.3082.557027460.30899.8
3.04-3.167.60.2433.153467030.24399.8
3.16-3.37.60.2063.752956940.206100
3.3-3.467.60.1624.649766540.162100
3.46-3.657.60.1395.347536230.13999.8
3.65-3.877.60.116.645525980.1199.9
3.87-4.147.60.0947.642475600.094100
4.14-4.477.60.0778.939565200.077100
4.47-4.97.60.0759.335174630.07599.9
4.9-5.487.50.0769.333234420.076100
5.48-6.337.50.0977.629123860.09799.9
6.33-7.757.50.0769.424423240.076100
7.75-10.967.40.05611.719082590.05699.9
10.96-29.7870.0629.59711380.06295.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.45→29.775 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.907 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 14.061 / SU ML: 0.151 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.372 / ESU R Free: 0.243
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) THAT WAS USED IN CO-CRYSTALLIZATION HAS BEEN MODELED AT THE PUTATIVE ACTIVE SITE BASED ON CLEAR ELECTRON DENSITY IN THE ANOMALOUS DIFFERENCE FOURIER MAP. 5.AN UNIDENTIFIED LIGAND (UNL) HAS BEEN MODELED AT THE PUTATIVE ACTIVE SITE. 6.GLYCEROL (GOL) AND PEG FRAGMENTS (PEG AND PGE) FROM THE CRYSTALLIZATION SOLUTION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.222 578 4.8 %RANDOM
Rwork0.164 ---
obs0.167 12072 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.36 Å2 / Biso mean: 23.22 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å2-0.36 Å20 Å2
2---0.72 Å20 Å2
3---1.08 Å2
Refinement stepCycle: LAST / Resolution: 2.45→29.775 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2053 0 83 66 2202
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222175
X-RAY DIFFRACTIONr_bond_other_d0.0020.021508
X-RAY DIFFRACTIONr_angle_refined_deg1.4941.9822922
X-RAY DIFFRACTIONr_angle_other_deg0.89433657
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9025269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.07323.7596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.68215329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7131512
X-RAY DIFFRACTIONr_chiral_restr0.0880.2313
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212398
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02452
X-RAY DIFFRACTIONr_mcbond_it1.64831332
X-RAY DIFFRACTIONr_mcbond_other0.3723545
X-RAY DIFFRACTIONr_mcangle_it3.00152127
X-RAY DIFFRACTIONr_scbond_it5.1918843
X-RAY DIFFRACTIONr_scangle_it7.17911794
LS refinement shellResolution: 2.45→2.513 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 41 -
Rwork0.178 841 -
all-882 -
obs--99.77 %
Refinement TLS params.Method: refined / Origin x: 17.9469 Å / Origin y: 39.8202 Å / Origin z: 6.1579 Å
111213212223313233
T0.0191 Å20.0145 Å20.0193 Å2-0.022 Å20.0202 Å2--0.0293 Å2
L1.2437 °20.0104 °2-0.0714 °2-1.0315 °20.0367 °2--0.7003 °2
S-0.0683 Å °0.0283 Å °-0.0551 Å °-0.0437 Å °-0.0052 Å °-0.0159 Å °0.0117 Å °0.0528 Å °0.0735 Å °

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