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- PDB-4v7n: Glycocyamine kinase, beta-beta homodimer from marine worm Namalyc... -

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Basic information

Entry
Database: PDB / ID: 4v7n
TitleGlycocyamine kinase, beta-beta homodimer from marine worm Namalycastis sp., with transition state analog Mg(II)-ADP-NO3-glycocyamine.
ComponentsGlycocyamine kinase beta chain
KeywordsTRANSFERASE / phosphagen kinase / glycocyamine kinase / transition state analog / Kinase
Function / homology
Function and homology information


phosphocreatine biosynthetic process / creatine kinase activity / extracellular space / ATP binding
Similarity search - Function
ATP:guanido phosphotransferase, N-terminal / ATP:guanido phosphotransferase, N-terminal domain superfamily / ATP:guanido phosphotransferase, N-terminal domain / Phosphagen kinase N-terminal domain profile. / ATP:guanido phosphotransferase / ATP:guanido phosphotransferase, catalytic domain / ATP:guanido phosphotransferase, C-terminal catalytic domain / Phosphagen kinase C-terminal domain profile. / Glutamine synthetase/guanido kinase, catalytic domain
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / GUANIDINO ACETATE / NITRATE ION / Glycocyamine kinase beta chain
Similarity search - Component
Biological speciesNamalycastis sp. ST01 (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLim, K. / Pullalarevu, S. / Herzberg, O.
Citation
Journal: Biochemistry / Year: 2010
Title: Structural basis for the mechanism and substrate specificity of glycocyamine kinase, a phosphagen kinase family member.
Authors: Lim, K. / Pullalarevu, S. / Surabian, K.T. / Howard, A. / Suzuki, T. / Moult, J. / Herzberg, O.
#1: Journal: COMP.BIOCHEM.PHYSIOL. B: BIOCHEM.MOL.BIOL. / Year: 2005
Title: Isolation, characterization, and cDNA-derived amino acid sequence of glycocyamine kinase from the tropical marine worm Namalycastis sp.
Authors: Mizuta, C. / Tanaka, K. / Suzuki, T.
History
DepositionDec 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 3L2F, 3L2G
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 20, 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
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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_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.value / _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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AA: Glycocyamine kinase beta chain
AB: Glycocyamine kinase beta chain
AC: Glycocyamine kinase beta chain
AD: Glycocyamine kinase beta chain
AE: Glycocyamine kinase beta chain
AF: Glycocyamine kinase beta chain
AG: Glycocyamine kinase beta chain
AH: Glycocyamine kinase beta chain
AI: Glycocyamine kinase beta chain
AJ: Glycocyamine kinase beta chain
AK: Glycocyamine kinase beta chain
AL: Glycocyamine kinase beta chain
AM: Glycocyamine kinase beta chain
AN: Glycocyamine kinase beta chain
AO: Glycocyamine kinase beta chain
AP: Glycocyamine kinase beta chain
AQ: Glycocyamine kinase beta chain
AR: Glycocyamine kinase beta chain
BA: Glycocyamine kinase beta chain
BB: Glycocyamine kinase beta chain
BC: Glycocyamine kinase beta chain
BD: Glycocyamine kinase beta chain
BE: Glycocyamine kinase beta chain
BF: Glycocyamine kinase beta chain
BG: Glycocyamine kinase beta chain
BH: Glycocyamine kinase beta chain
BI: Glycocyamine kinase beta chain
BJ: Glycocyamine kinase beta chain
BK: Glycocyamine kinase beta chain
BL: Glycocyamine kinase beta chain
BM: Glycocyamine kinase beta chain
BN: Glycocyamine kinase beta chain
BO: Glycocyamine kinase beta chain
BP: Glycocyamine kinase beta chain
BQ: Glycocyamine kinase beta chain
BR: Glycocyamine kinase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,610,603180
Polymers1,587,90136
Non-polymers22,702144
Water86,0044774
1
AA: Glycocyamine kinase beta chain
AB: Glycocyamine kinase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,47810
Polymers88,2172
Non-polymers1,2618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
AC: Glycocyamine kinase beta chain
AD: Glycocyamine kinase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,47810
Polymers88,2172
Non-polymers1,2618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
AE: Glycocyamine kinase beta chain
AF: Glycocyamine kinase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,47810
Polymers88,2172
Non-polymers1,2618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
AG: Glycocyamine kinase beta chain
AH: Glycocyamine kinase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,47810
Polymers88,2172
Non-polymers1,2618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
AI: Glycocyamine kinase beta chain
AJ: Glycocyamine kinase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,47810
Polymers88,2172
Non-polymers1,2618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
AK: Glycocyamine kinase beta chain
AL: Glycocyamine kinase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,47810
Polymers88,2172
Non-polymers1,2618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
AM: Glycocyamine kinase beta chain
AN: Glycocyamine kinase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,47810
Polymers88,2172
Non-polymers1,2618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
AO: Glycocyamine kinase beta chain
AP: Glycocyamine kinase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,47810
Polymers88,2172
Non-polymers1,2618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
AQ: Glycocyamine kinase beta chain
AR: Glycocyamine kinase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,47810
Polymers88,2172
Non-polymers1,2618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
BA: Glycocyamine kinase beta chain
BB: Glycocyamine kinase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,47810
Polymers88,2172
Non-polymers1,2618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
BC: Glycocyamine kinase beta chain
BD: Glycocyamine kinase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,47810
Polymers88,2172
Non-polymers1,2618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
BE: Glycocyamine kinase beta chain
BF: Glycocyamine kinase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,47810
Polymers88,2172
Non-polymers1,2618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
13
BG: Glycocyamine kinase beta chain
BH: Glycocyamine kinase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,47810
Polymers88,2172
Non-polymers1,2618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
14
BI: Glycocyamine kinase beta chain
BJ: Glycocyamine kinase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,47810
Polymers88,2172
Non-polymers1,2618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
15
BK: Glycocyamine kinase beta chain
BL: Glycocyamine kinase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,47810
Polymers88,2172
Non-polymers1,2618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
16
BM: Glycocyamine kinase beta chain
BN: Glycocyamine kinase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,47810
Polymers88,2172
Non-polymers1,2618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
17
BO: Glycocyamine kinase beta chain
BP: Glycocyamine kinase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,47810
Polymers88,2172
Non-polymers1,2618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
18
BQ: Glycocyamine kinase beta chain
BR: Glycocyamine kinase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,47810
Polymers88,2172
Non-polymers1,2618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)243.11, 114.27, 259.90
Angle α, β, γ (deg.)90.00, 90.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 36 molecules AAABACADAEAFAGAHAIAJAKALAMANAOAPAQARBABBBCBDBEBFBGBHBIBJBKBL...

#1: Protein ...
Glycocyamine kinase beta chain


Mass: 44108.363 Da / Num. of mol.: 36
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Namalycastis sp. ST01 (invertebrata) / Gene: GK-beta, GK_beta / Plasmid: pGK_beta221 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21star(DE3) / References: UniProt: Q6AW42, EC: 2.7.3.1

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Non-polymers , 5 types, 4918 molecules

#2: Chemical...
ChemComp-NMG / GUANIDINO ACETATE / N-[AMINO(IMINO)METHYL]GLYCINE


Mass: 117.107 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: C3H7N3O2
#3: Chemical...
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: Mg
#5: Chemical...
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: NO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4774 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 22.5% polyethylene glycol monomethyl ether (PMME) 2000, 0.1M calcium acetate, 0.1M Tris HCl, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 610182 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 13.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 3.1 / % possible all: 81.2

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Processing

Software
NameClassification
MAR345dtbdata collection
PHASERphasing
PHENIXrefinement
X-GENdata reduction
X-GENdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1u6r and 1vrp

1u6r

1vrp


Resolution: 2.3→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Used twinning refinement with twin operator (-h,-k,l) in Phenix program. Estimated twin fraction was 0.31.
RfactorNum. reflectionSelection details
Rfree0.263 29437 random
Rwork0.197 --
obs-586126 -
Displacement parametersBiso mean: 28 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms53544 0 720 2411 56675
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_deg1.3
LS refinement shellResolution: 2.3→2.38 Å / Rfactor Rfree: 0.344 / Rfactor Rwork: 0.273

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