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- PDB-2fv7: Crystal structure of human ribokinase -

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Basic information

Entry
Database: PDB / ID: 2fv7
TitleCrystal structure of human ribokinase
ComponentsRibokinase
KeywordsTRANSFERASE / ribokinase / structural genomics / structural genomics consortium / sgc
Function / homology
Function and homology information


ribokinase / ribokinase activity / Pentose phosphate pathway / D-ribose catabolic process / pentose-phosphate shunt / ATP binding / metal ion binding / nucleus / identical protein binding / cytosol
Similarity search - Function
Ribokinase / Ribokinase/fructokinase / pfkB family of carbohydrate kinases signature 2. / Carbohydrate/purine kinase, PfkB, conserved site / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Ribokinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsRabeh, W.M. / Tempel, W. / Nedyalkova, L. / Arrowsmith, C. / Edwards, A. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of human ribokinase
Authors: Rabeh, W.M. / Tempel, W. / Nedyalkova, L. / Arrowsmith, C. / Edwards, A. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
History
DepositionJan 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Refinement description / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 30, 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_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.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_conn.ptnr2_label_seq_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 42MOLPROBITY STRUCTURE VALIDATION PROGRAMS : MOLPROBITY (KING, REDUCE, AND PROBE) AUTHORS : I.W. ...MOLPROBITY STRUCTURE VALIDATION PROGRAMS : MOLPROBITY (KING, REDUCE, AND PROBE) AUTHORS : I.W.DAVIS,J.M.WORD URL : HTTP://KINEMAGE.BIOCHEM.DUKE.EDU/MOLPROBITY/ AUTHORS : J.S.RICHARDSON,W.B.ARENDALL,D.C.RICHARDSON REFERENCE : NEW TOOLS AND DATA FOR IMPROVING : STRUCTURES, USING ALL-ATOM CONTACTS : METHODS IN ENZYMOLOGY. 2003;374:385-412. MOLPROBITY OUTPUT SCORES: ALL-ATOM CLASHSCORE : 9.46 (9.53 B<40) BAD ROTAMERS : 2.1% 10/485 (TARGET 0-1%) RAMACHANDRAN OUTLIERS : 0.0% 0/612 (TARGET 0.2%) RAMACHANDRAN FAVORED : 98.4% 602/612 (TARGET 98.0%)
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribokinase
B: Ribokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,24120
Polymers70,2922
Non-polymers94918
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: Ribokinase
hetero molecules

B: Ribokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,24120
Polymers70,2922
Non-polymers94918
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_745-x+2,y-1/2,-z1
Buried area4690 Å2
ΔGint-79 kcal/mol
Surface area24280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.530, 72.978, 90.958
Angle α, β, γ (deg.)90.00, 91.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Ribokinase /


Mass: 35145.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBKS, RBSK / Plasmid: p28a-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9H477, ribokinase

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Non-polymers , 5 types, 102 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 12 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.3 Å3/Da / Density % sol: 46.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 40% PEG-550MME, vapor diffusion, sitting drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 10, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 34881 / % possible obs: 99.3 % / Redundancy: 3 % / Rmerge(I) obs: 0.046 / Χ2: 1.145 / Net I/σ(I): 13.6
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID
2.1-2.1897.830.26134030.9991
2.18-2.2698.730.22634391.6861
2.26-2.3799.630.18734601.2081
2.37-2.4999.930.12234981.0111
2.49-2.6599.930.08434930.91
2.65-2.8599.930.065353111
2.85-3.1499.93.10.04434891.0031
3.14-3.5999.930.03535281.1971
3.59-4.5299.630.02735311.2711
4.52-5097.52.90.02435091.2071

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.8 Å19.74 Å
Translation2.8 Å19.74 Å
Phasing dmMethod: Solvent flattening and Histogram matching

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
DM5phasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT1.701data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entries 1RKS, 1VM7
Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.914 / WRfactor Rfree: 0.236 / WRfactor Rwork: 0.189 / SU B: 16.602 / SU ML: 0.194 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.245 / ESU R Free: 0.201 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2484 1770 5.115 %thin shells
Rwork0.1979 ---
all0.201 ---
obs0.201 34605 99.186 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 23.979 Å2
Baniso -1Baniso -2Baniso -3
1--0.083 Å20 Å2-0.018 Å2
2--0.062 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4524 0 70 84 4678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224665
X-RAY DIFFRACTIONr_bond_other_d0.0020.022973
X-RAY DIFFRACTIONr_angle_refined_deg1.4621.9866360
X-RAY DIFFRACTIONr_angle_other_deg0.91437354
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5285618
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.53425.301166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.54315758
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2331516
X-RAY DIFFRACTIONr_chiral_restr0.0820.2781
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025196
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02866
X-RAY DIFFRACTIONr_nbd_refined0.2060.2839
X-RAY DIFFRACTIONr_nbd_other0.1830.22971
X-RAY DIFFRACTIONr_nbtor_refined0.1680.22292
X-RAY DIFFRACTIONr_nbtor_other0.0860.22308
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2121
X-RAY DIFFRACTIONr_metal_ion_refined0.110.26
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2230.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.213
X-RAY DIFFRACTIONr_mcbond_it0.4931.53062
X-RAY DIFFRACTIONr_mcbond_other0.1041.51258
X-RAY DIFFRACTIONr_mcangle_it0.92624927
X-RAY DIFFRACTIONr_mcangle_other0.42423977
X-RAY DIFFRACTIONr_scbond_it1.53731627
X-RAY DIFFRACTIONr_scbond_other0.32531892
X-RAY DIFFRACTIONr_scangle_it2.5614.51431
X-RAY DIFFRACTIONr_scangle_other1.2864.53377
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection all% reflection obs (%)
2.1-2.1540.2941180.25824460.26257599.573
2.154-2.2130.2771180.25523340.256246299.594
2.213-2.2770.571180.40122130.412246094.756
2.277-2.3460.3291180.23621760.24231399.179
2.346-2.4230.2171180.21721600.217228199.868
2.423-2.5070.2561180.21921010.221222199.91
2.507-2.6010.2351180.20220160.204213599.953
2.601-2.7070.2531180.20219520.205207399.855
2.707-2.8260.2461180.2218470.2221965100
2.826-2.9630.212590.20118120.201187299.947
2.963-3.1210.2721180.19616890.201180999.889
3.121-3.3080.268590.19216550.195171599.942
3.308-3.5340.2251180.1814720.183159399.812
3.534-3.8120.219590.16814330.17149899.599
3.812-4.1690.228590.15513210.157138799.495
4.169-4.650.175590.14611960.147125999.682
4.65-5.3480.175590.15410390.155109999.909
5.348-6.4990.25590.1989030.20196799.483
6.499-8.9830.19590.1766760.17775098
8.983-3000.1943940.19445586.593
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.0286-0.2825-0.62661.77910.62961.3320.0602-0.13210.2849-0.0491-0.08410.1845-0.0842-0.08110.0238-0.1565-0.001-0.0222-0.0711-0.0402-0.091334.82844.718-8.675
21.16730.4705-0.23332.3829-0.79721.9905-0.0152-0.0168-0.08610.0782-0.02860.06240.287-0.13370.0438-0.0756-0.0351-0.0297-0.077-0.0124-0.14736.05950.05233.534
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 322
2X-RAY DIFFRACTION1A401 - 403
3X-RAY DIFFRACTION2B15 - 322

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