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- PDB-4a3w: Crystal structure of Archaemetzincin (AmzA) from Archaeoglobus fu... -

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Basic information

Entry
Database: PDB / ID: 4a3w
TitleCrystal structure of Archaemetzincin (AmzA) from Archaeoglobus fulgidus at 2.16 A resolution complexed with citrate
ComponentsARCHAEMETZINCIN
KeywordsHYDROLASE / METALLOPROTEASE / PROTEASE / METZINCIN / METAL- BINDING
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases) / metallopeptidase activity / proteolysis / zinc ion binding
Similarity search - Function
Peptidase M54, archaemetzincin, archaeal/bacterial / Peptidase M54, archaemetzincin / Peptidase family M54 / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / Archaemetzincin
Similarity search - Component
Biological speciesARCHAEOGLOBUS FULGIDUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsGraef, C. / Schacherl, M. / Baumann, U.
CitationJournal: Plos One / Year: 2012
Title: Crystal Structures of Archaemetzincin Reveal a Moldable Substrate-Binding Site.
Authors: Graef, C. / Schacherl, M. / Waltersperger, S. / Baumann, U.
History
DepositionOct 5, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2012Group: Database references / Other
Revision 2.0Dec 20, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_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_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

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Assembly

Deposited unit
A: ARCHAEMETZINCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2334
Polymers17,9131
Non-polymers3203
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)111.926, 111.926, 102.094
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-2003-

HOH

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Components

#1: Protein ARCHAEMETZINCIN


Mass: 17912.850 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea) / Description: DSM 4304 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O29917, Hydrolases
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details2-HYDROXYPROPANE-1,2,3-TRICARBOXYLATE (FLC): CITRATE ION

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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: 5.13 Å3/Da / Density % sol: 76 % / Description: NONE
Crystal growpH: 4 / Details: 0.9 M AMMONIUM SULFATE, 0.1 M CITRIC ACID PH 4.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.16→49.07 Å / Num. obs: 20756 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 12.9 % / Biso Wilson estimate: 41.53 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 17.12
Reflection shellResolution: 2.16→2.29 Å / Redundancy: 13.1 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 2.72 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZVS

3zvs


Resolution: 2.16→49.074 Å / SU ML: 0.25 / σ(F): 1.99 / Phase error: 18.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2202 1037 5 %
Rwork0.1941 --
obs0.1954 20753 99.77 %
Solvent computationShrinkage radii: 1.01 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.348 Å2 / ksol: 0.431 e/Å3
Displacement parametersBiso mean: 39.41 Å2
Baniso -1Baniso -2Baniso -3
1-3.8401 Å20 Å20 Å2
2--3.8401 Å20 Å2
3----7.6802 Å2
Refinement stepCycle: LAST / Resolution: 2.16→49.074 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1229 0 15 72 1316
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081275
X-RAY DIFFRACTIONf_angle_d1.0671722
X-RAY DIFFRACTIONf_dihedral_angle_d14.424490
X-RAY DIFFRACTIONf_chiral_restr0.066198
X-RAY DIFFRACTIONf_plane_restr0.005221
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1602-2.27410.23271420.23722697X-RAY DIFFRACTION98
2.2741-2.41650.23721450.21582769X-RAY DIFFRACTION100
2.4165-2.60310.21521460.19982773X-RAY DIFFRACTION100
2.6031-2.86510.24041470.20612792X-RAY DIFFRACTION100
2.8651-3.27960.24141490.19762816X-RAY DIFFRACTION100
3.2796-4.13160.21061490.18742846X-RAY DIFFRACTION100
4.1316-49.08660.20931590.18423023X-RAY DIFFRACTION100

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