[English] 日本語
Yorodumi
- PDB-4hcf: Crystal Structure of Uncharacterized Cupredoxin-like Domain Prote... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4hcf
TitleCrystal Structure of Uncharacterized Cupredoxin-like Domain Protein Cupredoxin_1 with Copper Bound from Bacillus anthracis
ComponentsCupredoxin 1
KeywordsOXIDOREDUCTASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / beta-fold / beta sandwich / greek-key beta barrel
Function / homology
Function and homology information


EfeO-type cupredoxin-like domain / Cupredoxin-like domain / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / EfeO-type cupredoxin-like domain-containing protein / EfeO-type cupredoxin-like domain-containing protein
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.703 Å
AuthorsKim, Y. / Maltseva, N. / Shatsman, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of Uncharacterized Cupredoxin-like Domain Protein Cupredoxin_1 with Copper Bound from Bacillus anthracis
Authors: Kim, Y. / Maltseva, N. / Shatsman, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionSep 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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_asym_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_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_leaving_atom_flag / _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_label_asym_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: Cupredoxin 1
B: Cupredoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4015
Polymers22,1772
Non-polymers2233
Water2,162120
1
A: Cupredoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2483
Polymers11,0891
Non-polymers1602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cupredoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1522
Polymers11,0891
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Cupredoxin 1
hetero molecules

B: Cupredoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4015
Polymers22,1772
Non-polymers2233
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_656x+1,y,z+11
Buried area1110 Å2
ΔGint-22 kcal/mol
Surface area9480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.275, 73.594, 40.366
Angle α, β, γ (deg.)90.00, 116.72, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Cupredoxin 1


Mass: 11088.687 Da / Num. of mol.: 2 / Fragment: UNP residues 33-129
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames / Gene: BA_1561, GBAA_1561 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q81ST4, UniProt: A0A6L7H6L8*PLUS
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.28 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 120 mM magnessium sulfate, 150 mM formate pH 4.0, 38.6 % w/v PEG1000, 10 mM copper chloride, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 13, 2012 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 21670 / Num. obs: 21670 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 17.68 Å2 / Rsym value: 0.107 / Net I/σ(I): 11.8
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.48 / Num. unique all: 1093 / Rsym value: 0.518 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIX(phenix.refine: 1.8.1_1161)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Structure of the same protein (cupredoxin_1) without copper bound

Resolution: 1.703→30.43 Å / SU ML: 0.17 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 20.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1108 5.12 %random
Rwork0.177 ---
all0.179 21620 --
obs0.179 21620 98.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.6 Å2
Refinement stepCycle: LAST / Resolution: 1.703→30.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1440 0 7 120 1567
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081475
X-RAY DIFFRACTIONf_angle_d1.1991990
X-RAY DIFFRACTIONf_dihedral_angle_d12.165570
X-RAY DIFFRACTIONf_chiral_restr0.088241
X-RAY DIFFRACTIONf_plane_restr0.004246
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.703-1.78050.2241140.1982433254793
1.7805-1.87430.23051280.179225882716100
1.8743-1.99170.23331520.17625672719100
1.9917-2.14550.22031530.163525812734100
2.1455-2.36130.19541360.168126092745100
2.3613-2.70280.21811540.184825632717100
2.7028-3.40460.20631350.1852593272899
3.4046-30.43490.19911360.1742578271498
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)
18.0598-5.05714.44035.1726-0.99684.1106-0.11910.1462-0.2176-0.01520.0761-0.495-0.05150.21020.1710.13390.00310.02120.2164-0.01920.21620.31640.565149.2498
24.4185-2.72552.86632.3362-1.44912.0317-0.14710.3459-0.08130.14620.0046-0.0014-0.66840.28750.06180.1461-0.04590.02240.19140.0210.16814.99926.658940.7215
30.8521.5999-1.93798.092-6.87586.5184-0.0411-0.04150.1086-0.2211-0.692-0.4837-0.19060.40250.6940.17430.0155-0.05620.16570.0150.173618.0649-5.54443.6391
40.09160.54170.66454.6025.65546.94230.0059-0.0184-0.40280.82360.1843-0.03591.00720.1638-0.36930.2341-0.012-0.00660.21040.00220.267117.5878-15.022154.5372
51.7415-3.05311.73625.3848-3.03961.7296-0.02320.1335-0.0868-0.0396-0.0982-0.11290.20680.07990.06340.1566-0.0094-0.00950.2003-0.0240.191417.68171.631652.6744
69.25122.4183-2.87332.6502-0.92015.3421-0.34310.04470.8478-0.40150.0569-0.1025-0.36710.21410.07460.2939-0.02210.01450.1525-0.00060.218512.656613.629246.2351
72.22720.1039-1.27832.1696-0.82790.98980.0810.1114-0.1975-0.2035-0.20880.4660.2228-0.0020.13550.18120.0036-0.01330.1766-0.01640.19677.0168-0.520549.3877
81.19770.01030.62219.7597-1.36912.8995-0.2128-0.2220.19110.75170.16930.4427-0.4464-0.21120.06170.12270.0040.02940.1842-0.02190.199514.03055.439855.1722
91.2804-1.92320.1995.78640.22941.21680.2192-0.1167-0.3572-0.4966-0.0230.46940.6140.1563-0.20210.1867-0.0184-0.00570.17030.03730.23299.9698-10.761747.3154
105.7445-1.33840.54425.44471.19856.85440.0855-0.11340.01770.2120.10770.39690.0092-0.679-0.31090.1257-0.0037-0.00540.16040.00830.12455.5425.888440.7265
111.9193-3.90110.32359.2034-1.17830.28150.01960.154-0.24480.30640.21340.2520.0930.0211-0.09470.20630-0.02940.1472-0.03770.174314.0958-9.097342.6493
121.6648-1.23160.329.2414-6.32275.03220.0339-0.3898-0.56560.88050.13440.24270.2133-0.1172-0.11880.28590.0004-0.02870.254-0.01040.2149-1.01342.652127.995
134.517-2.1408-1.04242.18780.26621.8164-0.21740.2894-0.3691-0.06420.0370.38350.1321-0.11460.05280.148-0.0035-0.00490.166-0.01360.179114.4774-1.647720.5206
142.2355-1.8314-0.63981.51930.52040.17430.22610.09290.1577-0.0052-0.2858-0.0416-0.1497-0.0176-0.05730.19570.04310.00790.1757-0.02830.225713.5989.617919.7741
152.930.0448-0.28348.4762-1.06340.990.0010.06150.3617-0.1680.11740.814-0.301-0.0896-0.04550.18060.0071-0.00970.16190.00380.20417.02077.223325.5375
167.9779-1.25331.92199.0391-1.09133.92560.22710.458-0.9382-0.1781-0.2184-0.23670.20230.28240.02070.2546-0.0075-0.00440.1667-0.03380.245116.2248-10.576925.2669
171.7375-0.4054-0.33269.08690.63731.2277-0.0268-0.05040.17310.33220.022-0.2144-0.08610.1648-0.04680.1408-0.0225-0.0060.1780.00670.151416.72033.686231.7117
184.6499-3.3378-1.01372.44310.62690.6443-0.19-0.0551-0.3052-0.00430.13390.1536-0.0918-0.0191-0.03140.2801-0.0299-0.02030.21760.02230.18427.852-2.357729.309
193.83042.5905-1.10682.0635-1.66713.00130.4162-0.68441.65160.4832-0.17360.522-0.0131-0.2836-0.41760.2746-0.05040.0880.2127-0.08920.42310.266718.485329.8438
205.8059-6.31162.13097.9578-1.61861.23360.04690.34380.636-0.9216-0.1312-0.9194-0.2346-0.01030.02520.165-0.01620.04530.1359-0.00150.133620.439210.634226.2312
218.09781.5033-1.26364.4616-2.58687.3733-0.2082-0.3434-0.02130.16570.0896-0.1180.39050.4495-0.07810.10150.0197-0.00410.1659-0.00190.15124.6212-2.382628.283
220.6591-2.35121.25159.976-4.56122.50.26240.05840.73010.0124-0.0051-0.7328-0.06480.02570.12770.2512-0.00390.04520.17750.01050.289417.765512.07621.874
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 41 through 49 )
2X-RAY DIFFRACTION2chain 'A' and (resid 50 through 54 )
3X-RAY DIFFRACTION3chain 'A' and (resid 55 through 60 )
4X-RAY DIFFRACTION4chain 'A' and (resid 61 through 65 )
5X-RAY DIFFRACTION5chain 'A' and (resid 66 through 72 )
6X-RAY DIFFRACTION6chain 'A' and (resid 73 through 77 )
7X-RAY DIFFRACTION7chain 'A' and (resid 78 through 91 )
8X-RAY DIFFRACTION8chain 'A' and (resid 92 through 101 )
9X-RAY DIFFRACTION9chain 'A' and (resid 102 through 112 )
10X-RAY DIFFRACTION10chain 'A' and (resid 113 through 121 )
11X-RAY DIFFRACTION11chain 'A' and (resid 122 through 128 )
12X-RAY DIFFRACTION12chain 'B' and (resid 33 through 42 )
13X-RAY DIFFRACTION13chain 'B' and (resid 43 through 54 )
14X-RAY DIFFRACTION14chain 'B' and (resid 55 through 61 )
15X-RAY DIFFRACTION15chain 'B' and (resid 62 through 72 )
16X-RAY DIFFRACTION16chain 'B' and (resid 73 through 77 )
17X-RAY DIFFRACTION17chain 'B' and (resid 78 through 91 )
18X-RAY DIFFRACTION18chain 'B' and (resid 92 through 101 )
19X-RAY DIFFRACTION19chain 'B' and (resid 102 through 106 )
20X-RAY DIFFRACTION20chain 'B' and (resid 107 through 112 )
21X-RAY DIFFRACTION21chain 'B' and (resid 113 through 121 )
22X-RAY DIFFRACTION22chain 'B' and (resid 122 through 128 )

+
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://pdbjlvh1.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