[English] 日本語
Yorodumi
- PDB-2fqp: Crystal structure of a cupin domain (bp2299) from bordetella pert... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2fqp
TitleCrystal structure of a cupin domain (bp2299) from bordetella pertussis tohama i at 1.80 A resolution
Componentshypothetical protein BP2299Hypothesis
KeywordsMETAL BINDING PROTEIN / Double-stranded beta-helix fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / : / Cupin_2 domain-containing protein
Similarity search - Component
Biological speciesBordetella pertussis Tohama I (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of (np_880937.1) from BORDETELLA PERTUSSIS at 1.80 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJan 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 25, 2023Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type / 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_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.conn_type_id / _struct_conn.id / _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_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_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV ROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: hypothetical protein BP2299
B: hypothetical protein BP2299
C: hypothetical protein BP2299
D: hypothetical protein BP2299
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,44713
Polymers43,7114
Non-polymers7369
Water5,008278
1
A: hypothetical protein BP2299
B: hypothetical protein BP2299
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1056
Polymers21,8562
Non-polymers2494
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-90 kcal/mol
Surface area9300 Å2
MethodPISA
2
C: hypothetical protein BP2299
D: hypothetical protein BP2299
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3437
Polymers21,8562
Non-polymers4875
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-90 kcal/mol
Surface area9210 Å2
MethodPISA
3
C: hypothetical protein BP2299
D: hypothetical protein BP2299
hetero molecules

A: hypothetical protein BP2299
B: hypothetical protein BP2299
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,44713
Polymers43,7114
Non-polymers7369
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area6150 Å2
ΔGint-185 kcal/mol
Surface area17440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.919, 92.651, 53.058
Angle α, β, γ (deg.)90.00, 106.40, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: ARG / Refine code: 5

Dom-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1ALAAA3 - 954 - 96
2LYSBB3 - 944 - 95
3ALACC3 - 954 - 96
4ALADD3 - 954 - 96

-
Components

#1: Protein
hypothetical protein BP2299 / Hypothesis


Mass: 10927.838 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis Tohama I (bacteria)
Species: Bordetella pertussis / Strain: Tohama I / Gene: np_880937.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / References: GenBank: 33593293, UniProt: Q7VWF8*PLUS
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 1.83 Å3/Da / Density % sol: 36.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 8.5
Details: 0.2M NaOAc, 30.0% PEG-4000, 0.1M TRIS pH 8.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.019867, 0.979741
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 11, 2005
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0198671
20.9797411
ReflectionResolution: 1.8→19 Å / Num. obs: 27712 / % possible obs: 90.3 % / Redundancy: 4.1 % / Biso Wilson estimate: 13.16 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 11.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsRsym value
1.8-1.8594.640.3022.2421250.302
1.85-1.992.640.2632.6520680.263
1.9-1.9593.740.2023.4819990.202
1.95-2.0192.240.1664.2419290.166
2.01-2.0892.84.10.1454.9518490.145
2.08-2.15924.10.1176.118090.117
2.15-2.2390.64.10.1046.817230.104
2.23-2.3292.14.10.0967.7416690.096
2.32-2.4390.44.10.0848.6215870.084
2.43-2.5589.74.20.0769.7715150.076
2.55-2.6890.44.20.06411.6214120.064
2.68-2.8588.54.20.05114.2213250.051
2.85-3.04884.30.04316.9312420.043
3.04-3.2987.24.30.03819.3511630.038
3.29-3.687.14.30.03321.6510530.033
3.6-4.0286.24.40.03122.919440.031
4.02-4.6585.84.30.02824.48210.028
4.65-5.6984.14.40.0324.566860.03
5.69-8.0582.44.40.03622.715290.036
8.05-1973.64.20.03625.462640.036

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
SCALAdata scaling
PDB_EXTRACT1.601data extraction
SOLVEphasing
SHARPphasing
DMphasing
RESOLVEphasing
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.8→19 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.746 / SU ML: 0.079 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.147 / ESU R Free: 0.136
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: (1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2) THERE IS A METAL ION BOUND IN EACH MONOMER. IT IS ASSIGNED AS ZN2+ BASED ON AN X-RAY EMISSION SPECTRUM AND AN X-RAY FLUORESCENCE ...Details: (1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2) THERE IS A METAL ION BOUND IN EACH MONOMER. IT IS ASSIGNED AS ZN2+ BASED ON AN X-RAY EMISSION SPECTRUM AND AN X-RAY FLUORESCENCE SCAN NEAR ZN ABSORPTION EDGE. (3) THERE IS AN ACETATE ION IN EACH MONOMER BOUND NEAR ZN2+ ION. (4) THERE IS A PENTAETHYLENE GLYCOL 238 (N=5) MOLECULE BOUND IN THE STRUCTURE. THE SOURCE OF PENTAETHYLENE GLYCOL IS UNCERTAIN. IT MAY COME FROM THE CONTAMINATION OF PEG400 USED IN THE EXPERIMENT. IT IS ALSO POSSIBLE THAT WE ONLY OBSERVE THE ORDERED PART OF PEG400 AND THE REST OF PEG400 IS DISORDERED. (5) ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.202 1401 5.1 %RANDOM
Rwork0.154 ---
all0.156 ---
obs0.156 27688 89.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.089 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20 Å2-0.03 Å2
2---0.63 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2956 0 36 278 3270
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223109
X-RAY DIFFRACTIONr_bond_other_d0.0010.022813
X-RAY DIFFRACTIONr_angle_refined_deg1.5381.9594248
X-RAY DIFFRACTIONr_angle_other_deg0.76536553
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8615385
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.2123.481135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.12515483
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0541524
X-RAY DIFFRACTIONr_chiral_restr0.090.2474
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023454
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02602
X-RAY DIFFRACTIONr_nbd_refined0.1890.2472
X-RAY DIFFRACTIONr_nbd_other0.1840.22761
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21459
X-RAY DIFFRACTIONr_nbtor_other0.0830.21996
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2238
X-RAY DIFFRACTIONr_metal_ion_refined0.0250.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0980.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2030.291
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.224
X-RAY DIFFRACTIONr_mcbond_it2.14332050
X-RAY DIFFRACTIONr_mcbond_other0.7643769
X-RAY DIFFRACTIONr_mcangle_it2.66653186
X-RAY DIFFRACTIONr_scbond_it4.61181281
X-RAY DIFFRACTIONr_scangle_it6.238111062
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A504MEDIUM POSITIONAL0.20.5
2B504MEDIUM POSITIONAL0.240.5
3C504MEDIUM POSITIONAL0.270.5
4D504MEDIUM POSITIONAL0.310.5
1A827LOOSE POSITIONAL0.765
2B827LOOSE POSITIONAL0.575
3C827LOOSE POSITIONAL0.525
4D827LOOSE POSITIONAL0.645
1A504MEDIUM THERMAL1.182
2B504MEDIUM THERMAL1.072
3C504MEDIUM THERMAL1.132
4D504MEDIUM THERMAL1.192
1A827LOOSE THERMAL2.3810
2B827LOOSE THERMAL2.5310
3C827LOOSE THERMAL2.5310
4D827LOOSE THERMAL2.1110
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 122 -
Rwork0.144 2002 -
obs-2124 94.36 %
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)
10.16560.25780.20880.5160.19120.4195-0.01020.01410.0024-0.01060.0191-0.0013-0.02290-0.0089-0.02970.00040.008-0.01030.0011-0.015516.7344111.650464.3426
20.31120.27910.16070.59640.02050.5289-0.0235-0.02350.0129-0.01820.0616-0.00290.0753-0.0084-0.038-0.0129-0.0091-0.0027-0.01860.003-0.023411.744389.799258.7854
30.11340.02980.02450.8929-0.03450.3438-0.0103-0.00120.0091-0.00190.00280.04930.05910.00130.0075-0.018-0.00540.0016-0.0145-0.0049-0.020537.444689.078332.9547
40.60740.21220.05470.5314-0.06040.4296-0.02950.0209-0.00450.06150.0342-0.0098-0.0505-0.0245-0.0047-0.02580.0060.002-0.01610.0018-0.023341.3823111.043438.7508
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA0 - 951 - 96
22BB3 - 944 - 95
33CC0 - 951 - 96
44DD3 - 964 - 97

+
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