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- PDB-3m33: The crystal structure of a functionally unknown protein from Dein... -

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Basic information

Entry
Database: PDB / ID: 3m33
TitleThe crystal structure of a functionally unknown protein from Deinococcus radiodurans R1
ComponentsUncharacterized protein
KeywordsStructural Genomics / Unknown function / PSI-2 / protein structure initiative / MCSG / Midwest Center for Structural Genomics
Function / homologyVaccinia Virus protein VP39 / methyltransferase activity / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Methyltransferase domain-containing protein
Function and homology information
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.195 Å
AuthorsTan, K. / Mack, J. / Feldmann, B. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a functionally unknown protein from Deinococcus radiodurans R1
Authors: Tan, K. / Mack, J. / Feldmann, B. / Joachimiak, A.
History
DepositionMar 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2010Provider: 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 / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,12619
Polymers50,6342
Non-polymers1,49217
Water1,76598
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,20911
Polymers25,3171
Non-polymers89210
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9178
Polymers25,3171
Non-polymers6007
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,41822
Polymers50,6342
Non-polymers1,78420
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Buried area5710 Å2
ΔGint-211 kcal/mol
Surface area19650 Å2
MethodPISA
4
B: Uncharacterized protein
hetero molecules

B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,83416
Polymers50,6342
Non-polymers1,20014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Buried area4660 Å2
ΔGint-78 kcal/mol
Surface area19960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.579, 104.579, 125.880
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein Uncharacterized protein


Mass: 25317.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Strain: R1 / Gene: DR_0468 / Plasmid: pMCSG19b / Production host: Escherichia coli (E. coli) / Strain (production host): pPK1037 / References: UniProt: Q9RX47
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 3.92 Å3/Da / Density % sol: 68.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES, 1.26M (NH4)2SO4, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97911, 0.97962
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 7, 2010 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979111
20.979621
ReflectionResolution: 2.2→35 Å / Num. all: 38704 / Num. obs: 38704 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 42.4
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.747 / Mean I/σ(I) obs: 3.25 / Num. unique all: 1940 / Rsym value: 0.194 / % possible all: 96

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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: 2.195→34.232 Å / SU ML: 0.32 / σ(F): 0.04 / Phase error: 21.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2144 1851 5.05 %random
Rwork0.1808 ---
obs0.1825 36652 91.85 %-
all-36652 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.006 Å2 / ksol: 0.367 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.3104 Å20 Å20 Å2
2---0.3104 Å2-0 Å2
3---0.6208 Å2
Refinement stepCycle: LAST / Resolution: 2.195→34.232 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3320 0 82 98 3500
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083489
X-RAY DIFFRACTIONf_angle_d1.1264759
X-RAY DIFFRACTIONf_dihedral_angle_d18.621246
X-RAY DIFFRACTIONf_chiral_restr0.07482
X-RAY DIFFRACTIONf_plane_restr0.004620
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1949-2.27330.27611840.2153143X-RAY DIFFRACTION83
2.2733-2.36430.24771520.20043214X-RAY DIFFRACTION85
2.3643-2.47190.24581770.19533264X-RAY DIFFRACTION87
2.4719-2.60220.23441840.19453396X-RAY DIFFRACTION90
2.6022-2.76520.2451600.20413446X-RAY DIFFRACTION91
2.7652-2.97850.2371770.20633570X-RAY DIFFRACTION94
2.9785-3.27810.25722110.20043637X-RAY DIFFRACTION97
3.2781-3.75190.22151960.17323743X-RAY DIFFRACTION99
3.7519-4.7250.16761970.14293732X-RAY DIFFRACTION98
4.725-34.23570.18022130.16253656X-RAY DIFFRACTION95
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)
11.06840.6449-0.20571.60150.28641.11860.1233-0.080.05630.037-0.11830.15490.043-0.10240.00870.257-0.03730.02630.33930.0010.314610.564943.967114.3533
21.34180.0554-0.15451.7790.17511.26910.04970.17560.1636-0.1097-0.01750.21460.0062-0.2519-0.02390.29590.0308-0.06410.31610.05880.333411.913851.8614-8.9263
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA5 - 215
2X-RAY DIFFRACTION2chain BB7 - 216

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