[English] 日本語
Yorodumi
- PDB-3kw0: Crystal structure of Cysteine peptidase (NP_982244.1) from BACILL... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3kw0
TitleCrystal structure of Cysteine peptidase (NP_982244.1) from BACILLUS CEREUS ATCC 10987 at 2.50 A resolution
ComponentsCysteine peptidaseCysteine protease
KeywordsHYDROLASE / Cysteine peptidase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyPermuted papain-like amidase enzyme, YaeF/YiiX, C92 family / Permuted papain-like amidase enzyme, YaeF/YiiX, C92 family / endopeptidase domain like (from Nostoc punctiforme) / endopeptidase fold (from Nostoc punctiforme) / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta / LYSINE / Uncharacterized protein
Function and homology information
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Plos One / Year: 2011
Title: Structural Analysis of Papain-Like NlpC/P60 Superfamily Enzymes with a Circularly Permuted Topology Reveals Potential Lipid Binding Sites.
Authors: Xu, Q. / Rawlings, N.D. / Chiu, H.J. / Jaroszewski, L. / Klock, H.E. / Knuth, M.W. / Miller, M.D. / Elsliger, M.A. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A.
History
DepositionNov 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jul 17, 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 1.5Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_dist_value / _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_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_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cysteine peptidase
B: Cysteine peptidase
C: Cysteine peptidase
D: Cysteine peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,15717
Polymers99,2494
Non-polymers90813
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7800 Å2
ΔGint-150 kcal/mol
Surface area29390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.960, 64.960, 407.800
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A4 - 58
2112B4 - 58
3112C4 - 58
4112D4 - 58
1212A60 - 145
2212B60 - 145
3212C60 - 145
4212D60 - 145
1312A150 - 195
2312B150 - 195
3312C150 - 195
4312D150 - 195

-
Components

#1: Protein
Cysteine peptidase / Cysteine protease


Mass: 24812.273 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 10987 / Gene: BCE_A0238 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q74NK7
#2: Chemical
ChemComp-LYS / LYSINE / Lysine


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H15N2O2
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.8M KH2PO4, 0.8M NaH2PO4, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97942
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 20, 2007 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double Crystal Monochrometer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 2.5→37.774 Å / Num. obs: 33303 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 69.316 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 15.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsRsym value% possible all
2.5-2.645.71.0371.72750548071.03799.7
2.64-2.85.80.62432667846070.62499.8
2.8-2.995.80.3645.12520643420.36499.9
2.99-3.235.80.1968.82351140440.19699.6
3.23-3.545.80.10715.52139436900.10799.8
3.54-3.955.70.06623.91920433500.06699.8
3.95-4.565.60.05231.91662929690.05299.6
4.56-5.595.60.0534.41397625020.0599.6
5.59-7.915.60.05435.61078919380.05499.5
7.91-37.7745.50.04740.8579410540.04798.1

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→37.769 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 20.296 / SU ML: 0.201 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.45 / ESU R Free: 0.245
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. A LYSINE (LYS) WAS TENTATIVELY MODELED INTO THE ACTIVE SITE OF EACH MONOMER BASED ON DENSITY, PUTATIVE FUNCTION AND LIGAND-PROTEIN INTERACTIONS. CHLORIDE (CL) MODELED ARE PRESENT IN CRYSTALLIZATION CONDITIONS. 5. RAMACHANDRAN OUTLIERS (B1, B170 AND C170) ARE LOCATED IN REGIONS WHERE THE DENSITIES ARE POOR. THE DENSITIES FOR REGIONS 145-150 ARE ALSO POOR.
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1689 5.1 %RANDOM
Rwork0.192 ---
obs0.193 33302 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 116.76 Å2 / Biso mean: 44.038 Å2 / Biso min: 17.79 Å2
Baniso -1Baniso -2Baniso -3
1-1.88 Å20.94 Å20 Å2
2--1.88 Å20 Å2
3----2.82 Å2
Refinement stepCycle: LAST / Resolution: 2.5→37.769 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5992 0 49 41 6082
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0226152
X-RAY DIFFRACTIONr_bond_other_d0.0020.024021
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.9488306
X-RAY DIFFRACTIONr_angle_other_deg1.00939872
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6425771
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.86225.358293
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.951151070
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9321520
X-RAY DIFFRACTIONr_chiral_restr0.0830.2945
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026901
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021203
X-RAY DIFFRACTIONr_mcbond_it1.50633847
X-RAY DIFFRACTIONr_mcbond_other0.32931592
X-RAY DIFFRACTIONr_mcangle_it2.95256176
X-RAY DIFFRACTIONr_scbond_it4.63382305
X-RAY DIFFRACTIONr_scangle_it7.176112127
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1067TIGHT POSITIONAL0.070.05
2B1067TIGHT POSITIONAL0.080.05
3C1067TIGHT POSITIONAL0.060.05
4D1067TIGHT POSITIONAL0.080.05
1A1255MEDIUM POSITIONAL0.070.1
2B1255MEDIUM POSITIONAL0.080.1
3C1255MEDIUM POSITIONAL0.070.1
4D1255MEDIUM POSITIONAL0.080.1
1A1067TIGHT THERMAL0.270.5
2B1067TIGHT THERMAL0.280.5
3C1067TIGHT THERMAL0.30.5
4D1067TIGHT THERMAL0.30.5
1A1255MEDIUM THERMAL0.31
2B1255MEDIUM THERMAL0.31
3C1255MEDIUM THERMAL0.31
4D1255MEDIUM THERMAL0.31
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 113 -
Rwork0.39 2299 -
all-2412 -
obs--99.75 %
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)
11.17560.3483-0.86171.3888-0.64864.02520.1898-0.04250.02630.1525-0.04940.1144-0.4769-0.0748-0.14030.39780.1083-0.03130.04740.01020.1458-20.087115.780941.6917
20.4373-0.9447-0.23322.54960.08854.03060.01890.03510.04050.1519-0.0315-0.00530.02670.27630.01260.23050.129-0.02920.11050.02070.1838-30.944742.493135.5239
31.5083-1.44470.3282.88650.09913.63260.16560.2471-0.0514-0.1339-0.19640.0068-0.0310.18770.03080.20140.1326-0.04130.1180.00630.1473-12.749910.72385.4874
41.366-0.4566-0.0392.34340.31933.3358-0.00620.0958-0.09240.0010.1514-0.0560.05440.0628-0.14530.12810.1319-0.00650.17490.02430.1396-32.559732.8353-0.5881
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 195
2X-RAY DIFFRACTION1A201
3X-RAY DIFFRACTION2B-3 - 195
4X-RAY DIFFRACTION2B201
5X-RAY DIFFRACTION3C-4 - 195
6X-RAY DIFFRACTION3C201
7X-RAY DIFFRACTION4D0 - 195
8X-RAY DIFFRACTION4D201

+
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