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- PDB-3pu2: Crystal Structure of the Q3J4M4_RHOS4 protein from Rhodobacter sp... -

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Basic information

Entry
Database: PDB / ID: 3pu2
TitleCrystal Structure of the Q3J4M4_RHOS4 protein from Rhodobacter sphaeroides. Northeast Structural Genomics Consortium Target RhR263.
Componentsuncharacterized protein
KeywordsStructure Genomics / unknown function / SRPBCC superfamily / PSI-Biology / NESG / RhR263 / Structural Genomics / Protein Structure Initiative / Northeast Structural Genomics Consortium / Putative activator of Hsp90 ATPase 1 family
Function / homologyActivator of Hsp90 ATPase homologue 1-like / Activator of Hsp90 ATPase homolog 1-like protein / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta / Activator of Hsp90 ATPase homologue 1/2-like C-terminal domain-containing protein
Function and homology information
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.606 Å
AuthorsVorobiev, S. / Chen, Y. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Wang, D. / Everett, J.K. / Nair, R. / Acton, T.B. ...Vorobiev, S. / Chen, Y. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Wang, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of the Q3J4M4_RHOS4 protein from Rhodobacter sphaeroides.
Authors: Vorobiev, S. / Chen, Y. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Wang, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionDec 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Structure summary
Revision 1.3Nov 27, 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: uncharacterized protein
B: uncharacterized protein
C: uncharacterized protein
D: uncharacterized protein
E: uncharacterized protein
F: uncharacterized protein
G: uncharacterized protein
H: uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)148,1608
Polymers148,1608
Non-polymers00
Water1,29772
1
A: uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)18,5201
Polymers18,5201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)18,5201
Polymers18,5201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)18,5201
Polymers18,5201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)18,5201
Polymers18,5201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)18,5201
Polymers18,5201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)18,5201
Polymers18,5201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)18,5201
Polymers18,5201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)18,5201
Polymers18,5201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.214, 35.856, 230.468
Angle α, β, γ (deg.)90.000, 98.980, 90.000
Int Tables number3
Space group name H-MP121
Detailsmonomer,21.19 kD,91.7%

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Components

#1: Protein
uncharacterized protein


Mass: 18520.023 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: ATCC 17023/2.4.1/NCIB 8253/DSM 158 / Gene: RHOS4_06920, RSP_2105 / Plasmid: pET 21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) +Magic / References: UniProt: Q3J4M4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
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: 2.07 Å3/Da / Density % sol: 40.63 %
Crystal growTemperature: 291 K / Method: microbatch under paraffin oil / pH: 6
Details: 24% PEG 20000, 0.1M potassium bromide, 0.1M MES, pH 6.0, microbatch under paraffin oil, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97915 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 29, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 72214 / Num. obs: 68098 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.7 % / Biso Wilson estimate: 45.72 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 12.9
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 2.3 / Num. unique all: 7163 / % possible all: 72.3

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Processing

Software
NameVersionClassificationNB
PHENIX1.6_289refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.606→29.097 Å / Occupancy max: 1 / Occupancy min: 0.26 / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 0.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.263 3402 5.02 %RANDOM
Rwork0.23 ---
obs0.231 67784 93.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.4 Å2 / ksol: 0.311 e/Å3
Displacement parametersBiso max: 194.37 Å2 / Biso mean: 66.915 Å2 / Biso min: 8.37 Å2
Baniso -1Baniso -2Baniso -3
1-14.283 Å20 Å25.294 Å2
2--3.825 Å2-0 Å2
3----21.945 Å2
Refinement stepCycle: LAST / Resolution: 2.606→29.097 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9279 0 0 72 9351
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0119536
X-RAY DIFFRACTIONf_angle_d1.51713007
X-RAY DIFFRACTIONf_chiral_restr0.1131462
X-RAY DIFFRACTIONf_plane_restr0.0111684
X-RAY DIFFRACTIONf_dihedral_angle_d17.3343437
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.606-2.6430.354950.3221670176560
2.643-2.6820.274960.3232145224171
2.682-2.7240.3561290.312261239080
2.724-2.7690.433920.3032532262485
2.769-2.8170.3541310.3182514264590
2.817-2.8680.3561330.3232687282094
2.868-2.9230.3681450.3332770291596
2.923-2.9830.4111370.2992969310698
2.983-3.0470.3051440.2972715285998
3.047-3.1180.2951650.2722794295999
3.118-3.1960.321600.2942896305699
3.196-3.2820.3261460.2832886303299
3.282-3.3790.2581100.2452762287299
3.379-3.4880.251740.2162885305999
3.488-3.6120.2511750.2062899307499
3.612-3.7560.2211240.1992764288899
3.756-3.9270.2061760.1922838301499
3.927-4.1340.2321280.1892808293698
4.134-4.3920.2171490.1712916306599
4.392-4.7290.1721390.1512769290898
4.729-5.2030.1751650.1462853301898
5.203-5.950.2281480.1872816296498
5.95-7.4760.2451810.1992731291298
7.476-29.0980.2351600.232502266288
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)
10.9968-0.1194-0.63870.310.40351.721-0.1009-0.054-0.0575-0.0790.0324-0.07990.41920.1041-0.26450.2006-0.0086-0.07490.0657-0.02580.136176.769732.171685.3146
21.0063-0.39940.56220.7484-0.36910.8667-0.01880.1059-0.0634-0.32580.0497-0.1090.02210.1273-0.01840.3343-0.0635-0.02770.1569-0.02580.179555.274514.49928.8454
30.23420.10471.14931.7447-0.38542.4118-0.05380.00170.01390.095-0.0194-0.0797-0.1465-0.24090.03710.0294-0.0290.01360.083-0.00510.145550.167620.629758.4346
40.4112-0.79540.48441.14361.10691.7080.0668-0.0036-0.0536-0.37840.1535-0.1384-0.39980.3568-0.15450.2431-0.16810.12610.1664-0.07720.178282.507438.222555.7555
51.2687-0.3079-0.10720.4858-0.88681.9940.18570.008-0.07160.2044-0.26910.1368-0.10220.18330.05260.4375-0.06120.0340.1477-0.01170.185654.876322.20040.422
60.7777-0.15650.36031.3130.29731.26870.0527-0.04470.08550.3940.00170.0284-0.104-0.4166-0.06690.3504-0.03370.09520.33010.03520.242743.305112.647385.6772
70.8864-0.2855-0.71040.46340.62672.66590.2579-0.19880.0809-0.07670.0496-0.0064-0.45690.3718-0.2320.3609-0.07790.13040.1695-0.08880.133889.855630.007328.6492
81.4224-0.9853-0.68740.33830.24392.71270.1184-0.3630.19430.04020.0267-0.08480.38820.7979-0.16990.20640.0498-0.06780.4044-0.12870.200876.49437.8208114.2274
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA16 - 169
2X-RAY DIFFRACTION2chain BB15 - 169
3X-RAY DIFFRACTION3chain CC16 - 170
4X-RAY DIFFRACTION4chain DD16 - 169
5X-RAY DIFFRACTION5chain EE16 - 170
6X-RAY DIFFRACTION6chain FF16 - 170
7X-RAY DIFFRACTION7chain GG18 - 171
8X-RAY DIFFRACTION8chain HH16 - 170

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