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- PDB-3rob: The crystal structure of a conserved protein from Planctomyces li... -

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Basic information

Entry
Database: PDB / ID: 3rob
TitleThe crystal structure of a conserved protein from Planctomyces limnophilus DSM 3776
Componentsuncharacterized conserved protein
KeywordsStructural Genomics / unknown function / PSI-Biology / protein structure initiative / midwest center for structural genomics / MCSG
Function / homologyDomain of unknown function DUF4440 / Domain of unknown function (DUF4440) / Steroid delta5-4-isomerase / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / DUF4440 domain-containing protein
Function and homology information
Biological speciesPlanctomyces limnophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.48 Å
AuthorsTan, K. / Li, H. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a conserved protein from Planctomyces limnophilus DSM 3776
Authors: Tan, K. / Li, H. / Bearden, J. / Joachimiak, A.
History
DepositionApr 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 16, 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

Downloads & links

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Assembly

Deposited unit
A: uncharacterized conserved protein
B: uncharacterized conserved protein
C: uncharacterized conserved protein
D: uncharacterized conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7388
Polymers63,3694
Non-polymers3684
Water12,250680
1
A: uncharacterized conserved protein
B: uncharacterized conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8694
Polymers31,6852
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-24 kcal/mol
Surface area13590 Å2
MethodPISA
2
C: uncharacterized conserved protein
D: uncharacterized conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8694
Polymers31,6852
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-25 kcal/mol
Surface area13260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.098, 68.098, 124.520
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
DetailsExperimentally unknown. The chains A and B, C and D are predicted to form dimers, respectively.

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Components

#1: Protein
uncharacterized conserved protein


Mass: 15842.309 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Planctomyces limnophilus (bacteria) / Strain: DSM 3776 / Gene: Plim_4131 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: D5SZ41
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 680 / 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: 2.63 Å3/Da / Density % sol: 53.24 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Tris:HCl, 15% (v/v) Ethanol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97923 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 22, 2011 / Details: Mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 1.48→30 Å / Num. all: 107855 / Num. obs: 107855 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 38
Reflection shellResolution: 1.48→1.52 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 2.8 / Num. unique all: 5291 / % possible all: 99.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.48→29.487 Å / SU ML: 0.17 / σ(F): 0.01 / Phase error: 18.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1937 5254 5 %random
Rwork0.1722 ---
all0.1733 105018 --
obs0.1733 105018 97.29 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.011 Å2 / ksol: 0.381 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.3448 Å2-0 Å2-0 Å2
2--0.3448 Å20 Å2
3----0.6896 Å2
Refinement stepCycle: LAST / Resolution: 1.48→29.487 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4154 0 24 680 4858
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074356
X-RAY DIFFRACTIONf_angle_d1.0765910
X-RAY DIFFRACTIONf_dihedral_angle_d14.4071637
X-RAY DIFFRACTIONf_chiral_restr0.068663
X-RAY DIFFRACTIONf_plane_restr0.005770
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4784-1.53130.24044290.23989222X-RAY DIFFRACTION90
1.5313-1.59260.24164840.20859657X-RAY DIFFRACTION94
1.5926-1.66510.22264810.19319850X-RAY DIFFRACTION96
1.6651-1.75280.20275320.17959950X-RAY DIFFRACTION97
1.7528-1.86270.18875700.169510011X-RAY DIFFRACTION98
1.8627-2.00640.19635480.171310228X-RAY DIFFRACTION99
2.0064-2.20830.1975460.170110213X-RAY DIFFRACTION100
2.2083-2.52770.20285650.171310264X-RAY DIFFRACTION100
2.5277-3.1840.20015590.177210221X-RAY DIFFRACTION100
3.184-29.49320.16955400.156310148X-RAY DIFFRACTION99
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)
11.20990.6669-0.09950.9777-0.45480.76230.0469-0.0750.16820.04590.00570.0971-0.0594-0.0376-0.04860.06250.00340.01630.0766-0.00960.07692.642252.957837.1694
20.85390.2161-0.10091.3881-0.36010.5519-0.00140.0287-0.1347-0.06250.0216-0.11570.127-0.0146-0.00930.09980.0049-0.01230.0694-0.01640.0929-7.986430.968640.5844
30.8796-0.57620.04830.9568-0.72340.94910.03690.0837-0.1552-0.09220.0446-0.00270.1098-0.0885-0.0650.0764-0.014-0.02160.09-0.02380.087536.594443.088536.5452
40.539-0.28580.53071.328-0.42250.5064-0.06830.02880.08290.05550.0065-0.1435-0.14470.00920.05680.108-0.01810.0030.0823-0.00390.083325.953464.875432.1311
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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