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- PDB-3iuu: Crystal structure of Putative metallopeptidase (YP_676511.1) from... -

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Basic information

Entry
Database: PDB / ID: 3iuu
TitleCrystal structure of Putative metallopeptidase (YP_676511.1) from MESORHIZOBIUM SP. BNC1 at 2.13 A resolution
ComponentsPutative metallopeptidase
KeywordsHYDROLASE / YP_676511.1 / Putative metallopeptidase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


metallopeptidase activity / metal ion binding
Similarity search - Function
Microcystin LR degradation protein MlrC / Microcystin LR degradation protein MlrC, C-terminal / Microcystin LR degradation protein MlrC, N-terminal / MlrC C-terminus / Metallopeptidase family M81
Similarity search - Domain/homology
IMIDAZOLE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Microcystinase C
Similarity search - Component
Biological speciesMesorhizobium sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.13 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative metallopeptidase (YP_676511.1) from MESORHIZOBIUM SP. BNC1 at 2.13 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / 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 1.4Feb 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

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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)56,13817
Polymers54,5401
Non-polymers1,59816
Water5,657314
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.220, 82.220, 310.730
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Putative metallopeptidase / MlrC-like


Mass: 54539.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesorhizobium sp. (bacteria) / Strain: BNC1 / Gene: Meso_3979, YP_676511.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q11B79

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Non-polymers , 6 types, 330 molecules

#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.78 Å3/Da / Density % sol: 55.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.29
Details: 0.01 M cobalt chloride, 1.636 M ammonium sulfate, 0.1 M MES pH 6.29, Additive: 0.001 M MANGANESE CHLORIDE, 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 / Wavelength: 0.97883,0.91837
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 8, 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
10.978831
20.918371
ReflectionResolution: 2.13→46.829 Å / Num. obs: 36013 / % possible obs: 100 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 29.758 Å2 / Rmerge(I) obs: 0.165 / Net I/σ(I): 12.48
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.13-2.210.0112.53897336591100
2.21-2.290.0113.23419232061100
2.29-2.40.0113.73984836941100
2.4-2.520.0114.63603533491100
2.52-2.680.0115.83897936351100
2.68-2.890.0118.23879436231100
2.89-3.180.01112.33831435981100
3.18-3.640.01120.13840036311100
3.64-4.570.01128.23822436851100
4.57-46.8290.01132.2387624025199.7

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Phasing

PhasingMethod: MAD

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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: MAD / Resolution: 2.13→46.829 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.93 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 9.198 / SU ML: 0.111 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.197 / ESU R Free: 0.174
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. 4. SULFATE AND POLYETHYLENE GLYCOL FRAGMENTS MODELLED ARE PRESENT IN CYRO/CRYSTALLIZATION CONDITIONS. 5. ZINC AND IMIDAZOLE WERE TENTATIVELY MODELLED IN THE ACTIVE SITE. ZINC IS MODELED BASED ON DENSITY AN COORDINATION GEOMETRY. THE FINAL METAL ION ASSIGNMENT IS PENDING FOLLOW-UP STUDIES. IMIDAZOLE IS ASSIGNED BASED ON DENSITY, INTERACTION ENVIRONMENT AND PRESENCE IN THE PROTEIN BUFFER .
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1798 5 %RANDOM
Rwork0.184 ---
obs0.186 36013 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 99.05 Å2 / Biso mean: 22.601 Å2 / Biso min: 9.54 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20.36 Å20 Å2
2--0.72 Å20 Å2
3----1.07 Å2
Refinement stepCycle: LAST / Resolution: 2.13→46.829 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3786 0 88 314 4188
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223989
X-RAY DIFFRACTIONr_bond_other_d0.0010.022657
X-RAY DIFFRACTIONr_angle_refined_deg1.4991.975439
X-RAY DIFFRACTIONr_angle_other_deg0.9136446
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4615506
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.23523.167180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.51215612
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3041536
X-RAY DIFFRACTIONr_chiral_restr0.0880.2611
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214458
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02830
X-RAY DIFFRACTIONr_mcbond_it0.7111.52484
X-RAY DIFFRACTIONr_mcbond_other0.1921.51000
X-RAY DIFFRACTIONr_mcangle_it1.28624007
X-RAY DIFFRACTIONr_scbond_it2.24731505
X-RAY DIFFRACTIONr_scangle_it3.4394.51425
LS refinement shellResolution: 2.13→2.185 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 138 -
Rwork0.218 2453 -
all-2591 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 4.5634 Å / Origin y: 23.6196 Å / Origin z: 179.0097 Å
111213212223313233
T0.007 Å2-0.0173 Å2-0.0023 Å2-0.1136 Å2-0.0135 Å2--0.0331 Å2
L0.9063 °2-0.2293 °2-0.0724 °2-0.4421 °2-0.0155 °2--0.1491 °2
S0.0076 Å °0.0495 Å °-0.1348 Å °0.0348 Å °0.0002 Å °0.0244 Å °0.0017 Å °-0.007 Å °-0.0077 Å °

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