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- PDB-3o2i: The crystal structure of a functionally unknown protein from Lept... -

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Basic information

Entry
Database: PDB / ID: 3o2i
TitleThe crystal structure of a functionally unknown protein from Leptospirillum sp. Group II UBA
ComponentsUncharacterized protein
KeywordsStructural Genomics / Unknown function / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG
Function / homologyAlpha-Beta Plaits - #2710 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / DI(HYDROXYETHYL)ETHER / :
Function and homology information
Biological speciesLeptospirillum rubarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.197 Å
AuthorsZhang, R. / Tan, K. / Xu, X. / Cui, H. / Ng, J. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: The crystal structure of a functionally unknown protein from Leptospirillum sp. Group II UBA
Authors: Zhang, R. / Tan, K. / Xu, X. / Cui, H. / Ng, J. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionJul 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 6, 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 protein
B: Uncharacterized protein
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3365
Polymers44,0753
Non-polymers2602
Water3,009167
1
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5383
Polymers29,3842
Non-polymers1541
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-22 kcal/mol
Surface area10410 Å2
MethodPISA
2
C: Uncharacterized protein
hetero molecules

C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5964
Polymers29,3842
Non-polymers2122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area6060 Å2
ΔGint-14 kcal/mol
Surface area10010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.485, 91.630, 171.779
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Uncharacterized protein


Mass: 14691.816 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospirillum rubarum (bacteria) / Strain: Group II UBA / Gene: UBAL2_80490115 / Plasmid: p15Tv Lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A3ESP1
#2: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.25 Å3/Da / Density % sol: 45.42 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M MES, 20% PEG10K, 1/20 TEV, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929, 0.97943
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 27, 2010 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979291
20.979431
ReflectionResolution: 2.2→40 Å / Num. all: 20399 / Num. obs: 20399 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 25.7
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 3.4 / Num. unique all: 839 / % possible all: 84.7

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 2.197→39.314 Å / SU ML: 0.3 / σ(F): 0.04 / σ(I): 0 / Phase error: 24.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2508 982 5.15 %random
Rwork0.1938 ---
obs0.1967 19058 91.84 %-
all-19058 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.312 Å2 / ksol: 0.333 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.3932 Å20 Å2-0 Å2
2--2.738 Å20 Å2
3----12.1312 Å2
Refinement stepCycle: LAST / Resolution: 2.197→39.314 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2344 0 15 167 2526
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072421
X-RAY DIFFRACTIONf_angle_d0.9573272
X-RAY DIFFRACTIONf_dihedral_angle_d18.979864
X-RAY DIFFRACTIONf_chiral_restr0.068348
X-RAY DIFFRACTIONf_plane_restr0.004417
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1974-2.31320.30641180.21252102X-RAY DIFFRACTION77
2.3132-2.45810.28671360.20522390X-RAY DIFFRACTION86
2.4581-2.64790.26171320.19882545X-RAY DIFFRACTION91
2.6479-2.91420.29331410.19082617X-RAY DIFFRACTION93
2.9142-3.33580.25281600.20072685X-RAY DIFFRACTION97
3.3358-4.20190.21281580.16412792X-RAY DIFFRACTION98
4.2019-39.320.20151370.17122945X-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)
11.02431.1420.24551.345-0.09571.58990.0309-0.0462-0.0285-0.0292-0.02950.1603-0.12240.1498-0.00250.1479-0.03170.00220.2050.03690.20463.270132.599784.3591
23.04211.47531.94492.04411.27172.0229-1.13551.10830.1995-0.53810.86250.6213-0.65981.11070.14960.3884-0.3129-0.05390.45960.08420.1982-6.34129.189254.4108
34.02741.42572.46780.88390.70721.5831-0.56081.1645-0.1334-0.25580.5712-0.0557-0.46650.76850.01860.2623-0.2294-0.01870.481-0.00190.16683.075330.887858.7018
40.55570.52840.0370.666-0.23480.43650.0891-0.3919-0.3180.054-0.1474-0.06720.11430.22420.09150.16940.0137-0.01030.29690.08310.2639-1.087824.073189.3703
50.5710.0651.06710.40050.28132.21610.1574-0.0907-0.1231-0.13380.0581-0.0402-0.2044-0.0713-0.11420.2244-0.0475-0.03910.11780.04850.177724.45517.118655.7113
61.0005-0.04160.47960.60360.15110.39070.30140.1235-0.543-0.0069-0.05760.10460.13080.1718-0.16510.23890.1505-0.11030.1687-0.07730.25322.59078.278825.7817
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 5:71
2X-RAY DIFFRACTION2chain A and resid 72:97
3X-RAY DIFFRACTION3chain B and resid 5:71
4X-RAY DIFFRACTION4chain B and resid 72:99
5X-RAY DIFFRACTION5chain C and resid 5:71
6X-RAY DIFFRACTION6chain C and resid 72:97

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