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- PDB-3zvs: Crystal structure of Archaemetzincin (AmzA) from Archaeoglobus fu... -

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Basic information

Entry
Database: PDB / ID: 3zvs
TitleCrystal structure of Archaemetzincin (AmzA) from Archaeoglobus fulgidus at 1.4 A resolution complexed with malonate
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
MALONATE ION / Archaemetzincin
Similarity search - Component
Biological speciesARCHAEOGLOBUS FULGIDUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.396 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
DepositionJul 27, 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
Revision 2.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ARCHAEMETZINCIN
B: ARCHAEMETZINCIN
C: ARCHAEMETZINCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,53913
Polymers53,7393
Non-polymers80110
Water14,052780
1
A: ARCHAEMETZINCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2485
Polymers17,9131
Non-polymers3354
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ARCHAEMETZINCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1464
Polymers17,9131
Non-polymers2333
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ARCHAEMETZINCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1464
Polymers17,9131
Non-polymers2333
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.302, 63.490, 64.533
Angle α, β, γ (deg.)71.39, 86.68, 82.67
Int Tables number1
Space group name H-MP1

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Components

#1: Protein ARCHAEMETZINCIN


Mass: 17912.850 Da / Num. of mol.: 3
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.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 780 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.52 Å3/Da / Density % sol: 51.16 % / Description: NONE
Crystal growpH: 6 / Details: 18 % PEG 3350 0.2 M SODIUM MALONATE PH 6.0

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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: May 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→31.54 Å / Num. obs: 96247 / % possible obs: 91.8 % / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Biso Wilson estimate: 12.51 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 13.6
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 3.08 / % possible all: 85.8

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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 2XHQ

2xhq
PDB Unreleased entry


Resolution: 1.396→31.542 Å / SU ML: 0.13 / σ(F): 1.99 / Phase error: 16.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1636 1999 2.1 %
Rwork0.1437 --
obs0.1441 96244 91.88 %
Solvent computationShrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.038 Å2 / ksol: 0.427 e/Å3
Displacement parametersBiso mean: 15.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.5357 Å2-3.6061 Å2-1.8012 Å2
2--1.9246 Å20.9687 Å2
3----1.3889 Å2
Refinement stepCycle: LAST / Resolution: 1.396→31.542 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3711 0 34 780 4525
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123915
X-RAY DIFFRACTIONf_angle_d1.4345312
X-RAY DIFFRACTIONf_dihedral_angle_d12.781498
X-RAY DIFFRACTIONf_chiral_restr0.081617
X-RAY DIFFRACTIONf_plane_restr0.007686
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3957-1.44560.24961960.22658355X-RAY DIFFRACTION81
1.4456-1.50350.22711840.19489535X-RAY DIFFRACTION93
1.5035-1.57190.212000.1769536X-RAY DIFFRACTION93
1.5719-1.65470.20192080.15949650X-RAY DIFFRACTION94
1.6547-1.75840.18712030.15139638X-RAY DIFFRACTION94
1.7584-1.89420.16752050.14619536X-RAY DIFFRACTION93
1.8942-2.08480.18731990.14399492X-RAY DIFFRACTION92
2.0848-2.38630.15181930.13429428X-RAY DIFFRACTION92
2.3863-3.00620.16242110.13679483X-RAY DIFFRACTION93
3.0062-31.55010.12462000.12789592X-RAY DIFFRACTION94

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