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- PDB-4axq: CRYSTAL STRUCTURE OF ARCHAEMETZINCIN (AMZA) FROM ARCHAEOGLOBUS FU... -

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Basic information

Entry
Database: PDB / ID: 4axq
TitleCRYSTAL STRUCTURE OF ARCHAEMETZINCIN (AMZA) FROM ARCHAEOGLOBUS FULGIDUS AT 1.4 A RESOLUTION
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
Biological speciesARCHAEOGLOBUS FULGIDUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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
DepositionJun 13, 2012Deposition site: PDBE / Processing site: PDBE
SupersessionJun 27, 2012ID: 2XHQ
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2012Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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: ARCHAEMETZINCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3263
Polymers18,1951
Non-polymers1312
Water5,224290
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.339, 88.339, 50.275
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein ARCHAEMETZINCIN


Mass: 18195.127 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea) / Description: DSM-4304 / Plasmid: PET28A / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHREE RESIDUES AT THE N-TERMINUS ARE A REMAINDER OF THE CLEAVED 6XHIS TAG

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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: 54.88 % / Description: NONE
Crystal growpH: 7.5 / Details: 25% PEG 3350, 0.2 M (NH4)2SO4, 0.1 M HEPES PH 7.5

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→25.4 Å / Num. obs: 38202 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Biso Wilson estimate: 14.24 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.77
Reflection shellResolution: 1.4→1.48 Å / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.99 / % possible all: 98.6

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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 2X7M

2x7m


Resolution: 1.4→25.409 Å / SU ML: 0.12 / σ(F): 0 / Phase error: 18.13 / Stereochemistry target values: ML
Details: PHENIX.REFINE 1.8-1069 USED, WITH NEW BULK-SOLVENT AND ANISOTROPIC SCALING ALGORITHM GRID STEP FACTOR IN BULK SOLVENT CORRECTION 4.00.
RfactorNum. reflection% reflection
Rfree0.1864 2021 5.3 %
Rwork0.1641 --
obs0.1652 38201 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.3 Å2
Refinement stepCycle: LAST / Resolution: 1.4→25.409 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1273 0 2 290 1565
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081350
X-RAY DIFFRACTIONf_angle_d1.231835
X-RAY DIFFRACTIONf_dihedral_angle_d12.088517
X-RAY DIFFRACTIONf_chiral_restr0.078211
X-RAY DIFFRACTIONf_plane_restr0.005237
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.43510.26171400.23532571X-RAY DIFFRACTION100
1.4351-1.47380.23951400.20352559X-RAY DIFFRACTION100
1.4738-1.51720.23191420.18492582X-RAY DIFFRACTION100
1.5172-1.56620.23961430.17182578X-RAY DIFFRACTION100
1.5662-1.62210.21571430.16222552X-RAY DIFFRACTION100
1.6221-1.68710.19361470.16292601X-RAY DIFFRACTION100
1.6871-1.76380.20871440.15572549X-RAY DIFFRACTION100
1.7638-1.85680.1751480.15342560X-RAY DIFFRACTION100
1.8568-1.97310.18111400.15142597X-RAY DIFFRACTION100
1.9731-2.12540.16151420.14682586X-RAY DIFFRACTION100
2.1254-2.33910.17741430.15122588X-RAY DIFFRACTION100
2.3391-2.67730.20151490.15922606X-RAY DIFFRACTION100
2.6773-3.37190.17731460.1712612X-RAY DIFFRACTION100
3.3719-25.4130.17211540.16722639X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0738-0.1188-0.01440.19740.07280.1229-0.0583-0.09050.01670.07190.1144-0.05630.10310.02960.00670.1217-0.0044-0.01190.13680.01190.1104-12.50224.35347.0546
20.0393-0.03630.01990.0632-0.06790.07390.1498-0.28190.19290.2259-0.00670.05240.01560.0584-00.1316-0.0046-0.00950.1526-0.0220.1135-15.062833.107811.2818
30.1034-0.09840.04380.40860.0860.07480.0034-0.0748-0.16950.0562-0.0318-0.19160.08390.10310.020.0828-0.0064-0.00880.16860.01080.1366-7.052926.1024.3956
40.1725-0.10320.01530.0615-0.00180.08960.04590.08830.0712-0.1354-0.1007-0.13060.08660.12470.00710.13230.0170.04550.13880.01130.1367-6.494531.797-11.9276
50.01570.009-0.0260.02180.01190.06840.0065-0.1533-0.02950.1339-0.043-0.13840.14830.13010.00090.14650.01010.00990.1050.00930.1217-12.065521.95921.0326
60.4141-0.29350.04220.2194-0.14450.57810.05850.0410.0522-0.0366-0.07030.00980.007-0.0079-0.00740.1158-0.00640.01390.087-0.00980.0948-14.234734.151-6.4937
70.0732-0.06120.01920.225-0.14560.092-0.0833-0.05610.027-0.05580.0967-0.0298-0.0499-0.06570.01940.10440.0036-0.00990.0939-0.01840.0908-20.065136.91673.5581
80.00650.0253-0.04290.1828-0.33150.6064-0.11050.00810.0649-0.19260.14840.15630.0919-0.1521-0.01180.1097-0.041-0.06080.13220.04310.1853-30.950928.9261-2.948
90.15810.03150.08810.12150.03730.0384-0.14010.05720.0853-0.29850.15170.2885-0.0621-0.0390.00040.1673-0.0216-0.03690.12520.02090.1451-27.037238.4006-1.8361
100.0434-0.0151-0.00060.03260.0430.06490.08130.0609-0.1441-0.00450.0990.2330.0588-0.04290.00750.0908-0.0004-0.00860.14910.06620.1934-34.067524.07824.2793
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID -3 - 11)
2X-RAY DIFFRACTION2CHAIN A AND (RESID 12 - 26)
3X-RAY DIFFRACTION3CHAIN A AND (RESID 27 - 42)
4X-RAY DIFFRACTION4CHAIN A AND (RESID 43 - 58)
5X-RAY DIFFRACTION5CHAIN A AND (RESID 59 - 69)
6X-RAY DIFFRACTION6CHAIN A AND (RESID 70 - 103)
7X-RAY DIFFRACTION7CHAIN A AND (RESID 104 - 122)
8X-RAY DIFFRACTION8CHAIN A AND (RESID 121 - 132)
9X-RAY DIFFRACTION9CHAIN A AND (RESID 133 - 151)
10X-RAY DIFFRACTION10CHAIN A AND (RESID 152 - 160)

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