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- PDB-2gu1: Crystal structure of a zinc containing peptidase from vibrio cholerae -

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Basic information

Entry
Database: PDB / ID: 2gu1
TitleCrystal structure of a zinc containing peptidase from vibrio cholerae
ComponentsZinc peptidase
KeywordsHYDROLASE / Zinc Peptidase / alpha/beta / beta barrel / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


peptidoglycan binding / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / metal ion binding / plasma membrane
Similarity search - Function
Opacity-associated protein A / Opacity-associated protein A LysM-like domain / Nuclear Transport Factor 2; Chain: A, - #350 / Csd3-like, second N-terminal domain / Csd3 second domain / Glucose Permease (Domain IIA) / Glucose Permease (Domain IIA) / : / Peptidase M23 / Peptidase family M23 ...Opacity-associated protein A / Opacity-associated protein A LysM-like domain / Nuclear Transport Factor 2; Chain: A, - #350 / Csd3-like, second N-terminal domain / Csd3 second domain / Glucose Permease (Domain IIA) / Glucose Permease (Domain IIA) / : / Peptidase M23 / Peptidase family M23 / Duplicated hybrid motif / Nuclear Transport Factor 2; Chain: A, / Distorted Sandwich / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Peptidoglycan DD-endopeptidase ShyB
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsSugadev, R. / Kumaran, D. / Swaminathan, S. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Proteins / Year: 2008
Title: Crystal structure of a putative lysostaphin peptidase from Vibrio cholerae.
Authors: Ragumani, S. / Kumaran, D. / Burley, S.K. / Swaminathan, S.
History
DepositionApr 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Zinc peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7693
Polymers40,6801
Non-polymers882
Water2,396133
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.382, 85.396, 53.404
Angle α, β, γ (deg.)90.00, 112.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Zinc peptidase


Mass: 40680.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: Q9KUL5, Hydrolases; Acting on peptide bonds (peptidases)
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 Tris, 20% PEG4000, 0.2M ammonium sulfate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X12C11.0059, 1.0094
SYNCHROTRONNSLS X29A21.1
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 2101CCDApr 17, 2006Mirror
ADSC QUANTUM 3152CCDApr 20, 2006Mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si IIIMADMx-ray1
2Si IIISINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.00591
21.00941
31.11
ReflectionResolution: 1.9→50 Å / Num. all: 31988 / Num. obs: 31988 / % possible obs: 92.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 13.1 Å2 / Rsym value: 0.106 / Net I/σ(I): 12.1
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2 % / Num. unique all: 1652 / Rsym value: 0.14 / % possible all: 52

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
SHARPphasing
ARP/wARPmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.9→32.24 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 142984.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Missing residues listed in remark 465 were not modeled due to lack of electron density. Atoms missing in some residues listed in remark 470 are due to lack of density for side chain atoms ...Details: Missing residues listed in remark 465 were not modeled due to lack of electron density. Atoms missing in some residues listed in remark 470 are due to lack of density for side chain atoms and the relevant residues were modeled as ALA.
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1987 6.9 %RANDOM
Rwork0.23 ---
obs0.23 28741 89.8 %-
all-28741 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.97 Å2 / ksol: 0.376497 e/Å3
Displacement parametersBiso mean: 33.6 Å2
Baniso -1Baniso -2Baniso -3
1--2.6 Å20 Å23.06 Å2
2--7.82 Å20 Å2
3----5.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 1.9→32.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2553 0 2 133 2688
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d25.4
X-RAY DIFFRACTIONc_improper_angle_d0.79
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.298 191 6.7 %
Rwork0.281 2651 -
obs--53.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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