[English] 日本語
Yorodumi
- PDB-3e11: Crystal structure of a predicted zincin-like metalloprotease (ace... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 300000000000
TitleCrystal structure of a predicted zincin-like metalloprotease (acel_2062) from acidothermus cellulolyticus 11b at 1.80 A resolution
Componentspredicted zincin-like metalloprotease
KeywordsUNKNOWN FUNCTION / Duf1025 family protein / zincin-like fold / conserved matrix metalloprotease motif / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Zincin-like - #20 / Zincin-like metallopeptidase / Zincin-like metallopeptidase superfamily / Zincin-like metallopeptidase / Zincin-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Metallopeptidase family protein
Similarity search - Component
Biological speciesAcidothermus cellulolyticus 11B (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of predicted zincin-like metalloprotease (YP_873820.1) from ACIDOTHERMUS CELLULOLYTICUS 11B at 1.80 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: predicted zincin-like metalloprotease
B: predicted zincin-like metalloprotease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1916
Polymers25,9922
Non-polymers1984
Water3,477193
1
A: predicted zincin-like metalloprotease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0552
Polymers12,9961
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: predicted zincin-like metalloprotease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1354
Polymers12,9961
Non-polymers1393
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.030, 58.820, 46.930
Angle α, β, γ (deg.)90.000, 93.510, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein predicted zincin-like metalloprotease


Mass: 12996.235 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidothermus cellulolyticus 11B (bacteria)
Description: SYNTHETIC GENE: The gene product was based on YP_873820.1 (predicted zincin-like metalloprotease) from Acidothermus cellulolyticus (strain ATCC43068/11B)
Gene: YP_873820.1, Acel_2062 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A0LWM4
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.17
Details: 24.0% polyethylene glycol 8000, 0.167M calcium acetate, 0.1M MES pH 6.17, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97949,0.91837,0.97879
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 13, 2008 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979491
20.918371
30.978791
ReflectionResolution: 1.8→29.437 Å / Num. obs: 19523 / % possible obs: 95.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 17.514 Å2 / Rmerge(I) obs: 0.063
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.8-1.860.481.745613422194.6
1.86-1.940.3642.252183921194.3
1.94-2.030.2323.149803737194.8
2.03-2.130.1744.444743389194.3
2.13-2.270.1235.751473873195.1
2.27-2.440.1026.847853584195.5
2.44-2.690.0738.950003759195.9
2.69-3.070.04611.848583642196.1
3.07-3.870.02817.550353748196.2
3.87-29.4370.02422.450103751196.1

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.004data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→29.437 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.5 / SU ML: 0.087 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.125
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. CALCIUM CATIONS AND ACETATE ANIONS FROM THE CRYSTALLIZATION CONDITIONS HAVE BEEN MODELED IN THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.204 1004 5.1 %RANDOM
Rwork0.175 ---
obs0.176 19518 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.273 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20 Å20.07 Å2
2---0.15 Å20 Å2
3----0.69 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.437 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1791 0 10 193 1994
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221894
X-RAY DIFFRACTIONr_bond_other_d0.0020.021760
X-RAY DIFFRACTIONr_angle_refined_deg1.3861.982595
X-RAY DIFFRACTIONr_angle_other_deg0.81834063
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8495244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.58923.78995
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.02115305
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9421516
X-RAY DIFFRACTIONr_chiral_restr0.0760.2299
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022159
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02385
X-RAY DIFFRACTIONr_nbd_refined0.2310.2416
X-RAY DIFFRACTIONr_nbd_other0.1880.21882
X-RAY DIFFRACTIONr_nbtor_refined0.1790.2935
X-RAY DIFFRACTIONr_nbtor_other0.080.21149
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2162
X-RAY DIFFRACTIONr_metal_ion_refined0.1980.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2510.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.216
X-RAY DIFFRACTIONr_mcbond_it0.8021.51208
X-RAY DIFFRACTIONr_mcbond_other0.2041.5474
X-RAY DIFFRACTIONr_mcangle_it1.21621911
X-RAY DIFFRACTIONr_scbond_it1.9333760
X-RAY DIFFRACTIONr_scangle_it2.9024.5676
LS refinement shellResolution: 1.801→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 69 -
Rwork0.228 1363 -
all-1432 -
obs--98.69 %
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)
11.0362-0.70230.90721.1114-1.02943.4461-0.03840.0052-0.0059-0.0545-0.0053-0.0640.21730.09310.04370.0370.00780.00720.0456-0.00890.057912.217915.78223.8917
21.5846-0.8402-1.00550.87290.6132.33720.00970.0680.0564-0.0412-0.00110.0206-0.1074-0.1206-0.00860.0415-0.0093-0.00790.03880.00020.05432.414729.395346.4923
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 1131 - 114
2X-RAY DIFFRACTION2BB0 - 1131 - 114

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more