[English] 日本語
Yorodumi
- PDB-2an9: Crystal Structure Of Oligomeric E.coli Guanylate Kinase In Comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2an9
TitleCrystal Structure Of Oligomeric E.coli Guanylate Kinase In Complex With GDP
ComponentsGuanylate kinase
KeywordsTRANSFERASE / GMP kinase / guanylate kinase / oligomeric
Function / homology
Function and homology information


guanylate kinase / guanylate kinase activity / phosphorylation / ATP binding / identical protein binding / cytosol
Similarity search - Function
Guanylate kinase / Guanylate Kinase phosphate binding domain / Guanylate Kinase phosphate binding domain / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. ...Guanylate kinase / Guanylate Kinase phosphate binding domain / Guanylate Kinase phosphate binding domain / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE / : / Guanylate kinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsHible, G. / Renault, L. / Schaeffer, F. / Christova, P. / Radulescu, A.Z. / Evrin, C. / Gilles, A.M. / Cherfils, J.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Calorimetric and crystallographic analysis of the oligomeric structure of Escherichia coli GMP kinase
Authors: Hible, G. / Renault, L. / Schaeffer, F. / Christova, P. / Radulescu, A.Z. / Evrin, C. / Gilles, A.M. / Cherfils, J.
History
DepositionAug 11, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 30, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 25, 2023Group: 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_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.pdbx_dist_value / _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_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_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: Guanylate kinase
B: Guanylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7838
Polymers47,2512
Non-polymers1,5316
Water3,333185
1
A: Guanylate kinase
B: Guanylate kinase
hetero molecules

A: Guanylate kinase
B: Guanylate kinase
hetero molecules

A: Guanylate kinase
B: Guanylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,34824
Polymers141,7546
Non-polymers4,59318
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area26870 Å2
ΔGint-94 kcal/mol
Surface area54440 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)68.225, 68.225, 151.272
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

-
Components

#1: Protein Guanylate kinase / / GMP kinase


Mass: 23625.725 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: gmk / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BLI5 / References: UniProt: P60546, guanylate kinase
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: 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
#4: Chemical ChemComp-GMP / GUANOSINE / Guanosine


Mass: 283.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O5
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.14 Å3/Da / Density % sol: 42.1 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 4% (w/v) PEG 3350, 40mM potassium thiocyanate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9793 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 4, 2003
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.35→20 Å / Num. all: 16498 / Num. obs: 16498 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12 % / Biso Wilson estimate: 43.7 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 28.8
Reflection shellResolution: 2.35→2.41 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.144 / Mean I/σ(I) obs: 16.4 / Num. unique all: 1172 / % possible all: 97.7

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EX7

1ex7


Resolution: 2.35→19.69 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.888 / SU B: 8.06 / SU ML: 0.196 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.716 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25762 833 5 %RANDOM
Rwork0.18488 ---
all0.18859 15672 --
obs0.18859 15672 99.59 %-
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: 17.622 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.35→19.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3290 0 98 185 3573
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0213460
X-RAY DIFFRACTIONr_bond_other_d0.0020.023080
X-RAY DIFFRACTIONr_angle_refined_deg1.4781.984690
X-RAY DIFFRACTIONr_angle_other_deg0.84837152
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4725408
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0820.2512
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023798
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02708
X-RAY DIFFRACTIONr_nbd_refined0.2170.2743
X-RAY DIFFRACTIONr_nbd_other0.2290.23527
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0850.22096
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2090.2178
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.140.26
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2850.283
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2290.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6361.52042
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.22223286
X-RAY DIFFRACTIONr_scbond_it2.00331418
X-RAY DIFFRACTIONr_scangle_it3.3264.51404
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 57 -
Rwork0.191 1115 -
obs-1172 97.7 %
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)
11.5323-1.0347-0.23512.66280.58312.07040.07330.19540.13050.0531-0.11310.16180.0163-0.17490.03980.078-0.01670.03220.1187-0.02850.105218.1857.6277.906
26.66650.31562.8749.68432.756710.14410.06040.4676-0.1444-0.4887-0.12440.26880.0328-0.07720.0640.18820.0820.06620.2043-0.02410.041623.4523.502-12.424
39.73734.6126-2.59245.77060.05792.9419-0.08050.8415-0.4784-0.62710.0172-0.14090.403-0.16360.06320.20780.01960.01760.1765-0.04180.219221.402-17.552-0.851
41.3509-0.33080.15412.9820.27542.52520.06490.0465-0.153-0.022-0.0571-0.09370.31270.0925-0.00780.0306-0.02650.03630.0895-0.04930.109818.0687.00528.586
57.5447-1.4973-2.97946.14081.039110.4914-0.0918-0.6063-0.07210.64890.04320.099-0.1352-0.23540.04860.1435-0.0684-0.01350.1358-0.07070.083918.70813.82348.972
65.3843-0.0215-1.83451.64842.55861.95280.3319-0.3530.13940.4243-0.2258-0.005-0.1806-0.0647-0.10610.15-0.0386-0.00560.08680.00550.25953.18427.66937.014
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 362 - 36
2X-RAY DIFFRACTION1AA87 - 12787 - 127
3X-RAY DIFFRACTION1AA159 - 206159 - 206
4X-RAY DIFFRACTION2AA37 - 8637 - 86
5X-RAY DIFFRACTION2AE6011
6X-RAY DIFFRACTION2AC6031
7X-RAY DIFFRACTION3AA128 - 158128 - 158
8X-RAY DIFFRACTION3AF6021
9X-RAY DIFFRACTION4BB2 - 362 - 36
10X-RAY DIFFRACTION4BB87 - 12787 - 127
11X-RAY DIFFRACTION4BB159 - 206159 - 206
12X-RAY DIFFRACTION5BB37 - 8637 - 86
13X-RAY DIFFRACTION5BG16011
14X-RAY DIFFRACTION5BD16031
15X-RAY DIFFRACTION6BB128 - 158128 - 158
16X-RAY DIFFRACTION6BH16021

+
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