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- PDB-3sjr: Crystal structure of conserved unkown function protein CV_1783 fr... -

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Basic information

Entry
Database: PDB / ID: 3sjr
TitleCrystal structure of conserved unkown function protein CV_1783 from Chromobacterium violaceum ATCC 12472
ComponentsUncharacterized protein
Keywordsstructural genomics / unknown function / PSI-Biology / MCSG / Midwest center for structural genomics
Function / homologyTopoisomerase I; Chain A, domain 4 - #90 / Domain of unknown function DUF5610 / Domain of unknown function (DUF5610) / Topoisomerase I; Chain A, domain 4 / Orthogonal Bundle / Mainly Alpha / DUF5610 domain-containing protein
Function and homology information
Biological speciesChromobacterium violaceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.94 Å
AuthorsChang, C. / Hatzos-Skintges, C. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of conserved unkown function protein CV_1783 from Chromobacterium violaceum ATCC 12472
Authors: Chang, C. / Hatzos-Skintges, C. / Clancy, S. / Joachimiak, A.
History
DepositionJun 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 20, 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


Theoretical massNumber of molelcules
Total (without water)77,6974
Polymers77,6974
Non-polymers00
Water724
1
A: Uncharacterized protein
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)38,8482
Polymers38,8482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-56 kcal/mol
Surface area12600 Å2
MethodPISA
2
C: Uncharacterized protein
D: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)38,8482
Polymers38,8482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-54 kcal/mol
Surface area11970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.366, 109.471, 151.599
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Uncharacterized protein


Mass: 19424.141 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum (bacteria) / Gene: CV_1783 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q7NX46
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.55 Å3/Da / Density % sol: 51.69 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10mM tri-Sodium Citrate, 33%(w/v) PEG6000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915, 0.97929
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 23, 2011
RadiationMonochromator: Si(111) double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979151
20.979291
ReflectionResolution: 2.95→50 Å / Num. all: 17117 / Num. obs: 17091 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 8.7 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 35
Reflection shellResolution: 2.95→3 Å / Redundancy: 9 % / Rmerge(I) obs: 0.834 / Mean I/σ(I) obs: 2.44 / Num. unique all: 842 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MLPHAREphasing
DMphasing
SHELXDEphasing
RESOLVEphasing
ARP/wARPmodel building
Cootmodel building
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 2.94→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.918 / Occupancy max: 1 / Occupancy min: 1 / SU B: 36.977 / SU ML: 0.314 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.381 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2674 867 5.1 %RANDOM
Rwork0.2259 ---
all0.228 17059 --
obs0.228 17059 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 151.66 Å2 / Biso mean: 90.6137 Å2 / Biso min: 55.52 Å2
Baniso -1Baniso -2Baniso -3
1-1.92 Å20 Å20 Å2
2--3.65 Å20 Å2
3----5.57 Å2
Refinement stepCycle: LAST / Resolution: 2.94→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3648 0 0 4 3652
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223703
X-RAY DIFFRACTIONr_angle_refined_deg1.2061.9755013
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6935463
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.32724.111180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.30815633
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8911533
X-RAY DIFFRACTIONr_chiral_restr0.0750.2574
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212809
X-RAY DIFFRACTIONr_mcbond_it0.4991.52334
X-RAY DIFFRACTIONr_mcangle_it0.95723684
X-RAY DIFFRACTIONr_scbond_it1.29731369
X-RAY DIFFRACTIONr_scangle_it2.3074.51329
LS refinement shellResolution: 2.944→3.02 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 70 -
Rwork0.279 1103 -
all-1173 -
obs-1173 99.15 %
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)
12.9039-0.8461-1.133219.94741.51720.5169-0.2848-0.6910.5114-0.16330.4928-0.65330.13170.2685-0.20810.2915-0.0934-0.11720.2727-0.0880.194.4208-11.4208130.759
23.6612-2.7241-2.0033.0233-0.00744.315-0.01450.0186-0.4565-0.0295-0.03630.23410.74380.05180.05080.5179-0.0803-0.10350.1172-0.09990.461615.7684-14.5714143.1344
34.913-1.5124-0.64884.9318-0.18484.2921-0.0316-0.58540.32330.24450.0418-0.4411-0.14920.1219-0.01020.2056-0.1153-0.03690.1393-0.01280.221815.5545-2.8256141.7635
49.8413-0.35730.6632.4899-1.75022.3380.42210.4309-1.189-0.2644-0.54550.1912-0.01460.26990.12340.3131-0.0337-0.07770.2208-0.15480.380210.6449-4.8524134.3595
51.6852-2.10141.63216.6079-2.43982.16370.18680.62430.2946-0.9954-0.5859-1.08620.26180.62830.39910.39620.0026-0.02210.6560.03480.554914.2781-16.1211125.1332
62.7647-1.6795-0.68628.78651.68773.7956-0.1187-0.1173-0.084-0.310.26610.1776-0.04640.0674-0.14740.1089-0.0757-0.06690.1067-0.00340.17432.9783-15.6585123.0096
724.1315-2.28473.23162.16680.16373.11090.81390.27490.7207-0.35-0.7118-0.40110.65090.393-0.10210.41230.0980.05540.41940.10960.402238.43593.3709133.4058
81.6684-0.3101-2.571911.42716.37367.4457-0.04540.20180.0819-0.2968-0.12731.0548-0.2454-0.23780.17270.11870.01780.03540.1979-0.00020.330736.589319.8451125.2927
94.4696-2.07610.25339.5169-0.19083.70480.2009-0.14180.1725-0.4082-0.1082-0.19770.01260.2315-0.09260.0249-0.01440.01190.10010.04320.107346.509418.3542123.46
102.2214.8071.446526.51215.08085.406-0.2848-0.2513-0.38580.88450.22190.6530.37160.12170.06290.38630.00610.08780.30310.08790.349245.600814.9011131.9007
1118.4516-0.45164.69125.66390.04368.4738-0.4962-0.42190.90870.08770.4077-0.0002-0.3568-0.110.08850.3212-0.08870.03090.09230.01650.230931.900512.8846133.2226
1211.6122-2.9105-0.1955.62451.03876.0861-0.102-1.514-0.51550.26010.330.22860.3299-0.2083-0.2280.2247-0.1345-0.00150.29830.0840.131832.96244.6436140.5011
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A48 - 74
2X-RAY DIFFRACTION2A75 - 109
3X-RAY DIFFRACTION3A110 - 172
4X-RAY DIFFRACTION4B48 - 74
5X-RAY DIFFRACTION5B75 - 109
6X-RAY DIFFRACTION6B110 - 172
7X-RAY DIFFRACTION7C48 - 74
8X-RAY DIFFRACTION8C75 - 109
9X-RAY DIFFRACTION9C110 - 172
10X-RAY DIFFRACTION10D48 - 74
11X-RAY DIFFRACTION11D75 - 109
12X-RAY DIFFRACTION12D110 - 172

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