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- PDB-2x7m: Crystal structure of Archaemetzincin (amzA) from Methanopyrus kan... -

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Basic information

Entry
Database: PDB / ID: 2x7m
TitleCrystal structure of Archaemetzincin (amzA) from Methanopyrus kandleri at 1.5 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 speciesMETHANOPYRUS KANDLERI (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsWaltersperger, S.M. / Widmer, C. / Baumann, U.
CitationJournal: Proteins / Year: 2010
Title: Crystal Structure of Archaemetzincin Amza from Methanopyrus Kandleri at 1.5A Resolution.
Authors: Waltersperger, S.M. / Widmer, C. / Baumann, U.
History
DepositionMar 1, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2011Group: Database references / Refinement description / Version format compliance
Revision 2.0May 8, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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

Downloads & links

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Assembly

Deposited unit
A: ARCHAEMETZINCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1623
Polymers22,0311
Non-polymers1312
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.510, 55.080, 58.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ARCHAEMETZINCIN


Mass: 22031.428 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHANOPYRUS KANDLERI (archaea) / Strain: AV19 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8TXW1, 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


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 39 % / Description: NONE
Crystal growpH: 7.6 / Details: PH 7.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 26660 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Biso Wilson estimate: 22.67 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.57
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 5 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.52 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.5_2)refinement
XDSdata reduction
XSCALEdata scaling
SHELXCDphasing
SHELXEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.5→40.03 Å / SU ML: 0.14 / σ(F): 1.99 / Phase error: 21.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.203 1324 5 %
Rwork0.176 --
obs0.178 26507 99.3 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.94 Å2 / ksol: 0.41 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-10.4123 Å2-0 Å2-0 Å2
2---3.2837 Å20 Å2
3----7.1286 Å2
Refinement stepCycle: LAST / Resolution: 1.5→40.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1429 0 2 103 1534
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121462
X-RAY DIFFRACTIONf_angle_d1.2861965
X-RAY DIFFRACTIONf_dihedral_angle_d17.287557
X-RAY DIFFRACTIONf_chiral_restr0.059216
X-RAY DIFFRACTIONf_plane_restr0.005254
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.56010.30021440.25142744X-RAY DIFFRACTION99
1.5601-1.63110.25341470.21722781X-RAY DIFFRACTION99
1.6311-1.71710.2271450.19452754X-RAY DIFFRACTION99
1.7171-1.82460.2371460.18922783X-RAY DIFFRACTION100
1.8246-1.96550.21021460.18082763X-RAY DIFFRACTION100
1.9655-2.16330.20541450.17712781X-RAY DIFFRACTION99
2.1633-2.47630.19261480.17812808X-RAY DIFFRACTION100
2.4763-3.11970.21971490.17622838X-RAY DIFFRACTION99
3.1197-40.04190.18071540.16342931X-RAY DIFFRACTION98
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)
10.02190.0078-0.03430.0004-0.01830.01790.13770.4897-0.52240.10480.05420.112-0.37850.09990.00020.44540.0753-0.01730.4156-0.04010.3611-10.709811.381410.4905
20.04990.02440.09030.033-0.00290.1487-0.0780.0070.08780.6993-0.36240.14810.251-0.28180.00010.242-0.05040.02430.2398-0.05420.32410.1679-6.57965.4347
30.49690.10490.24520.23850.08750.6679-0.1253-0.1286-0.10690.1956-0.03060.54610.0432-0.1762-0.00020.2628-0.01220.00390.2188-0.0190.22273.77430.176814.199
40.01630.0003-0.00520.00640.0102-0.0041-0.5459-0.26390.5656-0.0104-0.3366-0.13550.0187-0.66930.00020.3940.00760.18860.4604-0.24790.6519-5.68392.083912.4696
50.5625-0.10470.07080.2787-0.14360.29950.16120.34030.08070.0981-0.19450.23570.3771-0.1653-0.00170.1869-0.05440.00160.2461-0.09280.29523.8489-13.7356-3.7624
60.57130.48290.33960.39330.39490.78620.06180.3320.0465-0.0483-0.26420.1450.0067-0.29970.00010.13610.0205-0.00610.2716-0.02640.22282.0785-4.2716-2.5598
70.2948-0.1136-0.13420.37450.59840.68930.00680.04130.0284-0.16730.01260.0013-0.1182-0.008800.18440.00150.00210.20870.00670.194810.8426-3.6723-0.7458
80.3213-0.21030.18310.77781.01411.21480.08390.1322-0.00380.1865-0.04190.0004-0.37810.43140.00010.2359-0.0658-0.00550.25780.00840.197913.42013.53638.4462
90.5211-0.0355-0.62760.25760.34361.14280.1759-0.2408-0.0016-0.29840.0353-0.3892-1.06430.89520.02140.4689-0.13070.00850.2788-0.02340.25216.06939.83239.0558
100.0148-0.0482-0.06370.4640.17590.31110.66170.1086-0.1437-0.03470.6386-0.6341-0.2918-0.39560.01550.79370.24570.10440.28110.10830.33041.677618.68853.5747
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID -6:2)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 3:10)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 11:31)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 32:37)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 38:49)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 50:76)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 77:107)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 108:146)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 147:166)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 167:173)

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