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- PDB-3na2: Crystal Structure of Protein of Unknown Function from Mine Draina... -

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Basic information

Entry
Database: PDB / ID: 3na2
TitleCrystal Structure of Protein of Unknown Function from Mine Drainage Metagenome Leptospirillum rubarum
ComponentsUncharacterized protein
KeywordsStructural Genomics / Unknown function / beta-fold / metagenome / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyHeme iron utilization protein-like fold - #20 / Heme iron utilization protein-like fold / 3-Layer(aba) Sandwich / Alpha Beta / ACETIC ACID / DI(HYDROXYETHYL)ETHER / :
Function and homology information
Biological speciesLeptospirillum rubarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.293 Å
AuthorsKim, Y. / Xu, X. / Cui, H. / Chin, S. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crsystal Structure of Protein of Unknown Function from Mine Drainage Metagenome Leptospirillum rubarum
Authors: Kim, Y. / Xu, X. / Cui, H. / Chin, S. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionMay 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 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

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,0498
Polymers78,7174
Non-polymers3324
Water2,648147
1
A: Uncharacterized protein
hetero molecules

B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)39,5254
Polymers39,3582
Non-polymers1662
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_546-x+1/2,y-1/2,-z+11
Buried area2080 Å2
ΔGint-8 kcal/mol
Surface area13300 Å2
MethodPISA
2
D: Uncharacterized protein
hetero molecules

C: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)39,5254
Polymers39,3582
Non-polymers1662
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+1/2,y+1/2,-z1
Buried area2410 Å2
ΔGint-2 kcal/mol
Surface area12820 Å2
MethodPISA
3
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5254
Polymers39,3582
Non-polymers1662
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Uncharacterized protein
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5254
Polymers39,3582
Non-polymers1662
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.367, 115.047, 73.596
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-189-

HOH

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Components

#1: Protein
Uncharacterized protein


Mass: 19679.217 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospirillum rubarum (bacteria) / Strain: Group II UBA / Gene: UBAL2_80620259 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: A3EUC6
#2: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.05 Å3/Da / Density % sol: 40.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Sodium Cacodylate pH 6.5, 0.2 M Magnesium acetate, 20 % PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 4, 2010 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 29653 / Num. obs: 29653 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 37.09 Å2 / Rsym value: 0.11 / Net I/σ(I): 11.9
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 7.9 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 1447 / Rsym value: 0.791 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
RESOLVEmodel building
SOLVEphasing
PHENIXmodel building
PHENIX(phenix.refine: 1.6_289)refinement
HKL-3000data reduction
HKL-3000data scaling
RESOLVEphasing
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.293→36.24 Å / SU ML: 0.34 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 27.49 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1927 6.82 %random
Rwork0.186 ---
all0.19 28258 --
obs0.19 28258 94.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.004 Å2 / ksol: 0.346 e/Å3
Displacement parametersBiso mean: 53.8 Å2
Baniso -1Baniso -2Baniso -3
1-19.1945 Å2-0 Å2-0 Å2
2---8.7514 Å20 Å2
3----10.443 Å2
Refinement stepCycle: LAST / Resolution: 2.293→36.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4291 0 22 147 4460
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064478
X-RAY DIFFRACTIONf_angle_d0.9756073
X-RAY DIFFRACTIONf_dihedral_angle_d15.591687
X-RAY DIFFRACTIONf_chiral_restr0.069667
X-RAY DIFFRACTIONf_plane_restr0.005787
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.2934-2.37540.34381720.25932357252986
2.3754-2.47050.31431910.24642466265791
2.4705-2.58290.29831860.22292507269392
2.5829-2.7190.29021890.20972578276794
2.719-2.88930.31291850.2142616281196
2.8893-3.11230.27772010.20832670287197
3.1123-3.42520.22861960.18252689288597
3.4252-3.92040.2261910.15632733292498
3.9204-4.93730.17582030.13642801300499
4.9373-36.24420.24522130.18172914312799
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)
11.7115-0.53920.22421.2461-0.99461.7891-0.07790.01890.11690.26720.0039-0.01680.08270.2250.07040.31810.0429-0.02510.19620.02750.087714.273250.415326.1422
21.2070.0450.48750.60060.8582.32550.13180.1413-0.23840.16060.0956-0.05160.88530.0290.25210.7535-0.0746-0.09280.1914-0.07430.140428.941781.523536.9444
33.692-3.1484-0.22813.26521.412.4810.0787-0.28810.984-0.10060.2191-0.8032-0.4916-0.0954-0.25180.2831-0.02710.04240.1413-0.11590.389725.337447.7849-0.7022
41.9211.6227-0.44043.2736-0.71720.99410.0889-0.0108-0.22130.1984-0.1047-0.23230.19090.0707-0.05110.17090.0224-0.00080.20080.03530.161814.987978.938610.8588
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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