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- PDB-2rbc: Crystal structure of a putative ribokinase from Agrobacterium tum... -

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Basic information

Entry
Database: PDB / ID: 2rbc
TitleCrystal structure of a putative ribokinase from Agrobacterium tumefaciens
ComponentsSugar kinase
KeywordsTRANSFERASE / sugar kinase / ribokinase family / ATP-binding site / structural genomics / Agrobacterium tumefaciens / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


kinase activity / cytosol
Similarity search - Function
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
Biological speciesAgrobacterium tumefaciens str. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsCuff, M.E. / Xu, X. / Zheng, H. / Edwards, A.M. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: Structure of a putative ribokinase from Agrobacterium tumefaciens.
Authors: Cuff, M.E. / Xu, X. / Zheng, H. / Edwards, A.M. / Savchenko, A. / Joachimiak, A.
History
DepositionSep 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sugar kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,28413
Polymers37,3661
Non-polymers91812
Water7,206400
1
A: Sugar kinase
hetero molecules

A: Sugar kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,56826
Polymers74,7312
Non-polymers1,83624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area2520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.024, 81.024, 139.799
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-327-

CL

DetailsAuthors state that the biological unit of this protein is unknown, and that probably it is a dimer shown in remark 350.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Sugar kinase / AGR_C_4560p


Mass: 37365.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria)
Species: Agrobacterium tumefaciens / Strain: C58 / Gene: RbsK, AGR_C_4560, Atu2509 / Plasmid: Modified p11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q8UCH8, UniProt: A9CHQ7*PLUS, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor

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Non-polymers , 5 types, 412 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.07 Å3/Da / Density % sol: 59.94 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis-Tris pH 6.5, 1.5M Ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97873, 0.97886
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Apr 20, 2006
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978731
20.978861
ReflectionRedundancy: 13.2 % / Av σ(I) over netI: 9.9 / Number: 492007 / Rmerge(I) obs: 0.073 / Χ2: 1.36 / D res high: 1.9 Å / D res low: 50 Å / Num. obs: 37345 / % possible obs: 99.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.685098.210.0522.93311.8
3.724.6810010.0471.8212.9
3.253.7210010.0541.74213.5
2.953.2510010.0591.32914
2.742.9510010.0711.24514.2
2.582.7410010.081.14414.4
2.452.5810010.0951.07714.5
2.342.4510010.1090.99514.5
2.252.3410010.1641.25614.4
2.172.2510010.181.79414.4
2.112.1710010.1760.91914.7
2.052.1199.910.2030.92914.6
1.992.0510010.2440.91811.8
1.941.9999.810.3860.9369.5
1.91.9497.910.251.3028.5
ReflectionResolution: 1.9→50 Å / Num. all: 69844 / Num. obs: 69844 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 30.6 Å2 / Rmerge(I) obs: 0.059 / Χ2: 0.993 / Net I/σ(I): 9.9
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 6.3 / Num. unique all: 4637 / Χ2: 1.308 / % possible all: 98.4

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Phasing

PhasingMethod: MAD
Phasing MADD res high: 1.9 Å / D res low: 50 Å / FOM : 0.362 / FOM acentric: 0.388 / FOM centric: 0.183 / Reflection: 35714 / Reflection acentric: 31138 / Reflection centric: 4576
Phasing MAD set

Highest resolution: 1.9 Å / Lowest resolution: 50 Å

IDR cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
12.110.10.100311384576
20.970.938.812.40.320.28310424551
Phasing MAD set shell
IDResolution (Å)R cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
112.01-501.5710.40.2008284
16.82-12.011.4810.40.300491241
14.76-6.821.7910.40.2001261377
13.66-4.761.2110.30.2002404532
12.97-3.661.4710.20.1003886649
12.5-2.972.4310.10.1005673804
12.16-2.53.8610.10007180840
11.9-2.1613.2110.1000101611049
212.01-500.870.7711.114.10.970.668084
26.82-12.010.850.821012.50.90.63487237
24.76-6.820.910.849.813.40.760.541260377
23.66-4.760.950.91115.60.520.342403530
22.97-3.660.960.939.213.60.450.293883648
22.5-2.970.970.947.510.10.380.285667803
22.16-2.50.990.998.411.10.240.177144834
21.9-2.1611912.20.140.1101181038
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se38.51506-0.875-0.645-0.0740
2Se36.64563-0.862-0.665-0.180
3Se39.58156-1.119-0.574-0.0790
4Se34.83258-0.849-0.552-0.1580
5Se58.77821-0.825-0.61-0.120
6Se39.0239-1.064-0.753-0.1320
7Se39.12199-0.914-0.528-0.2050
8Se59.43863-0.962-0.898-0.1490
9Se66.28204-1.203-0.697-0.2510
10Se42.91651-0.875-0.645-0.074-0.054
11Se37.70619-0.861-0.665-0.18-0.044
12Se42.29323-1.119-0.574-0.079-0.054
13Se37.93235-0.849-0.552-0.158-0.046
14Se65.09966-0.825-0.609-0.12-0.056
15Se42.81662-1.064-0.753-0.132-0.047
16Se46.25343-0.914-0.528-0.205-0.025
17Se61.77279-0.963-0.899-0.149-0.027
18Se69.5309-1.203-0.697-0.251-0.026
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
12.01-500.5240.6780.3751668284
6.82-12.010.5890.7040.354732491241
4.76-6.820.6060.6820.35316381261377
3.66-4.760.5410.6010.27329362404532
2.97-3.660.5290.5770.2445353886649
2.5-2.970.4630.5020.18464775673804
2.16-2.50.3150.340.10680207180840
1.9-2.160.1690.1820.04511210101611049
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 35714
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.25-10047.90.831505
6.44-8.2536.80.923562
5.46-6.4442.90.906652
4.82-5.4645.10.924747
4.37-4.82440.933820
4.02-4.3746.50.929883
3.75-4.0246.50.91952
3.52-3.7546.80.925995
3.33-3.5247.20.8951069
3.17-3.3351.20.8881112
3.03-3.1750.30.8861172
2.91-3.0348.90.8981211
2.8-2.9147.70.8871244
2.7-2.8510.8881291
2.61-2.750.50.8911339
2.53-2.6153.20.881372
2.46-2.5351.90.8741404
2.39-2.4655.10.8681460
2.33-2.3956.90.8441463
2.27-2.3358.20.8361181
2.22-2.27640.8521573
2.17-2.22630.8171234
2.12-2.1762.20.8321595
2.08-2.1266.60.8321681
2.04-2.0869.60.8321746
2-2.0469.50.8231764
1.96-274.40.7491672
1.9-1.9677.10.6133015

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM5phasing
REFMACrefinement
PDB_EXTRACT3data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.9→32.17 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.933 / SU B: 6.809 / SU ML: 0.099 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.129
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: The Bijvoet differences were used in phasing. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1802 5 %RANDOM
Rwork0.188 ---
all0.19 35713 --
obs0.19 35713 95.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.905 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å20 Å20 Å2
2--0.83 Å20 Å2
3----1.67 Å2
Refinement stepCycle: LAST / Resolution: 1.9→32.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2295 0 52 400 2747
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222480
X-RAY DIFFRACTIONr_bond_other_d0.0010.021648
X-RAY DIFFRACTIONr_angle_refined_deg1.491.9783379
X-RAY DIFFRACTIONr_angle_other_deg0.94434015
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1065325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.51823.2100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.60315391
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4591521
X-RAY DIFFRACTIONr_chiral_restr0.0890.2385
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022800
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02496
X-RAY DIFFRACTIONr_nbd_refined0.210.2523
X-RAY DIFFRACTIONr_nbd_other0.2010.21838
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21215
X-RAY DIFFRACTIONr_nbtor_other0.0880.21332
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2298
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1930.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1270.220
X-RAY DIFFRACTIONr_mcbond_it1.3041.51885
X-RAY DIFFRACTIONr_mcbond_other0.2311.5643
X-RAY DIFFRACTIONr_mcangle_it1.32722541
X-RAY DIFFRACTIONr_scbond_it2.6783979
X-RAY DIFFRACTIONr_scangle_it3.5754.5838
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 131 -
Rwork0.362 2417 -
all-2548 -
obs--93.99 %
Refinement TLS params.Method: refined / Origin x: 22.4041 Å / Origin y: 0.1285 Å / Origin z: 19.7446 Å
111213212223313233
T-0.0755 Å20.0051 Å20.0019 Å2--0.0828 Å20.0248 Å2---0.0735 Å2
L0.952 °20.3421 °2-0.3958 °2-0.6633 °2-0.3053 °2--1.5371 °2
S0.0458 Å °-0.0107 Å °0.0536 Å °0.0214 Å °0.008 Å °0.0279 Å °0.0215 Å °-0.0294 Å °-0.0538 Å °

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