[English] 日本語
Yorodumi
- PDB-2hek: Crystal structure of O67745, a hypothetical protein from Aquifex ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2hek
TitleCrystal structure of O67745, a hypothetical protein from Aquifex aeolicus at 2.0 A resolution.
ComponentsHypothetical protein
KeywordsStructural Genomics / Unknown Function / Predominantly alpha helical protein with GDP binding site and active site being far from each other / PSI / Protein Structure Initiative / Berkeley Structural Genomics Center / BSGC
Function / homology
Function and homology information


dGTPase activity / dGTP catabolic process
Similarity search - Function
HD domain like / HD associated region / Hypothetical protein af1432 / Hypothetical protein af1432 / HD domain profile. / HD domain / HD domain / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Alpha-Beta Plaits ...HD domain like / HD associated region / Hypothetical protein af1432 / Hypothetical protein af1432 / HD domain profile. / HD domain / HD domain / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Alpha-Beta Plaits / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BROMIDE ION / GUANOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / HD domain-containing protein
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.997 Å
AuthorsOganesyan, V. / Jancarik, J. / Adams, P.D. / Kim, R. / Kim, S.H. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Structure of O67745_AQUAE, a hypothetical protein from Aquifex aeolicus.
Authors: Oganesyan, V. / Adams, P.D. / Jancarik, J. / Kim, R. / Kim, S.H.
History
DepositionJun 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2006Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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_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_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: Hypothetical protein
B: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,76424
Polymers88,3732
Non-polymers2,39122
Water6,395355
1
A: Hypothetical protein
B: Hypothetical protein
hetero molecules

A: Hypothetical protein
B: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,52948
Polymers176,7474
Non-polymers4,78244
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area21560 Å2
ΔGint-401 kcal/mol
Surface area56990 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)107.687, 144.413, 144.677
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsAsymmetric unit contains 2 polypeptides and each of two GDP molecules have contacts with both polypeptides. This information is used to call the asymmetric unit contents a biological assembly. Although it should be mentioned here that two such homodimers have also very intensive contact area. That symmetry operation is: -x,y,-z+1/2.

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Hypothetical protein /


Mass: 44186.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Plasmid: pB2.1275B / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12 / References: UniProt: O67745

-
Non-polymers , 7 types, 377 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 3.18 Å3/Da / Density % sol: 61.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 10 mg/ml protein was mixed with 1:1 ratio with reservoir consisted of: 200 mM NaCl, 100 mM Phosphate-Citrate buffer, 10% PEG 3000, 100 mM NaBr, 5% Glycerol, pH 4.2, VAPOR DIFFUSION, HANGING ...Details: 10 mg/ml protein was mixed with 1:1 ratio with reservoir consisted of: 200 mM NaCl, 100 mM Phosphate-Citrate buffer, 10% PEG 3000, 100 mM NaBr, 5% Glycerol, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 26, 2004
Details: Divergence: 3.0(h)x0.35(v) mrad Spot size: 0.140(h)x0.150(v) mm
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.997→43 Å / Num. all: 80115 / Num. obs: 76300 / % possible obs: 95.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.7 % / Biso Wilson estimate: 44 Å2 / Rsym value: 0.044 / Net I/σ(I): 21.4
Reflection shellResolution: 1.997→2.07 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.5 / Num. unique all: 8061 / Rsym value: 0.518 / % possible all: 95.7

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.997→12 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.99 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.273 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2201 3807 5 %RANDOM
Rwork0.17455 ---
all0.17686 75574 --
obs0.17686 71767 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 46.142 Å2
Baniso -1Baniso -2Baniso -3
1-2.27 Å20 Å20 Å2
2---1.03 Å20 Å2
3----1.24 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.997→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6218 0 132 355 6705
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0226476
X-RAY DIFFRACTIONr_angle_refined_deg1.4521.9918709
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4165736
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.44522.943333
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.866151207
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0011558
X-RAY DIFFRACTIONr_chiral_restr0.1050.2929
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024821
X-RAY DIFFRACTIONr_nbd_refined0.2150.22925
X-RAY DIFFRACTIONr_nbtor_refined0.310.24434
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2317
X-RAY DIFFRACTIONr_metal_ion_refined0.0860.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.224
X-RAY DIFFRACTIONr_mcbond_it4.04543825
X-RAY DIFFRACTIONr_mcangle_it5.13365965
X-RAY DIFFRACTIONr_scbond_it4.99543033
X-RAY DIFFRACTIONr_scangle_it5.61762744
X-RAY DIFFRACTIONr_rigid_bond_restr5.69836858
X-RAY DIFFRACTIONr_sphericity_free6.2153363
X-RAY DIFFRACTIONr_sphericity_bonded4.60336345
LS refinement shellResolution: 1.997→2.048 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 263 -
Rwork0.196 4802 -
obs-8061 92.55 %

+
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