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- PDB-3eo6: Crystal structure of protein of unknown function (DUF1255) (AFE_2... -

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Basic information

Entry
Database: PDB / ID: 3eo6
TitleCrystal structure of protein of unknown function (DUF1255) (AFE_2634) from ACIDITHIOBACILLUS FERROOXIDANS NCIB8455 at 0.97 A resolution
Componentsprotein of unknown function (DUF1255)
Keywordsstructural genomics / unknown function / AFE_2634 / protein of unknown function (DUF1255) / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyJelly Rolls / Jelly Rolls / Sandwich / Mainly Beta
Function and homology information
Biological speciesAcidithiobacillus ferrooxidans ATCC 23270 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 0.97 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of protein of unknown function (DUF1255) (AFE_2634) from ACIDITHIOBACILLUS FERROOXIDANS NCIB8455 at 0.97 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: software / struct_conn / struct_ref_seq
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: protein of unknown function (DUF1255)
B: protein of unknown function (DUF1255)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5255
Polymers23,3552
Non-polymers1713
Water7,602422
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-25 kcal/mol
Surface area10520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.785, 82.028, 40.847
Angle α, β, γ (deg.)90.000, 109.950, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Refine code: 6 / Auth seq-ID: 0 - 105 / Label seq-ID: 0 - 105

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein protein of unknown function (DUF1255)


Mass: 11677.310 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidithiobacillus ferrooxidans ATCC 23270 (bacteria)
Gene: AFE_2634 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 422 / Source method: isolated from a natural source / Formula: H2O
Sequence details(1) THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED ...(1) THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. (2) THE SEQUENCE IS NOT AVAILABLE IN THE UNIPROT-KB DATABASE AT THE TIME OF DEPOSITION. IT IS AVAILABLE AS LOCUS ID AFE_2634 FROM THE COMPREHENSIVE MICROBIAL RESOURCE AT THE J. CRAIG VENTER INSTITUTE.

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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: 2.08 Å3/Da / Density % sol: 40.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2000M MgCl2, 30.0000% PEG-4000, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97837
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 1, 2008 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.978371
ReflectionResolution: 0.97→28.194 Å / Num. obs: 111566 / % possible obs: 99.4 % / Redundancy: 4.1 % / Biso Wilson estimate: 7.317 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 5.911
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
0.97-13.50.7031.12885381650.70398
1-1.023.60.5161.52820979430.51698.3
1.02-1.053.60.3822751077360.3898.5
1.05-1.083.60.2892.62670474680.28998.9
1.08-1.123.60.2093.62635073430.20999.1
1.12-1.163.60.1614.62574171330.16199.3
1.16-1.23.60.1425.12491368850.14299.6
1.2-1.253.60.1335.32399766000.13399.7
1.25-1.313.70.1225.72331563850.12299.9
1.31-1.373.70.1086.42237360960.108100
1.37-1.453.70.0937.32141858030.093100
1.45-1.533.70.0798.52039355040.079100
1.53-1.643.70.0719.11924951450.071100
1.64-1.774.20.079.11992347870.07100
1.77-1.944.90.0738.42176144570.073100
1.94-2.176.30.0629.92519139940.062100
2.17-2.57.40.06210.62634435410.062100
2.5-3.077.50.05411.52240530010.054100
3.07-4.346.80.04812.91584423210.04899.9
4.34-28.946.20.0512.7774912590.0597.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHARPphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 0.97→28.194 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.978 / Occupancy max: 1 / Occupancy min: 0.11 / SU B: 0.613 / SU ML: 0.015 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.022 / ESU R Free: 0.022
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO ~0.8 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. U VALUES WERE REFINED INDIVIDUALLY 4. TRIS (TRS) AND MG MODELED WERE PRESENT IN CRYSTALLIZATION CONDITIONS. 5. THE DENSITY FOR N-TERMINUS AND C-TERMINUS ARE POOR.
RfactorNum. reflection% reflectionSelection details
Rfree0.143 5605 5 %RANDOM
Rwork0.123 ---
obs0.124 111533 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 46.85 Å2 / Biso mean: 11.791 Å2 / Biso min: 3.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å2-0.2 Å2
2---0.26 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 0.97→28.194 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2227 0 10 454 2691
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0212313
X-RAY DIFFRACTIONr_bond_other_d0.0010.021512
X-RAY DIFFRACTIONr_angle_refined_deg1.921.9833210
X-RAY DIFFRACTIONr_angle_other_deg0.97333740
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3255336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.19424.059101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.22615405
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6821519
X-RAY DIFFRACTIONr_chiral_restr0.1050.2349
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212872
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02463
X-RAY DIFFRACTIONr_mcbond_it2.25531499
X-RAY DIFFRACTIONr_mcbond_other1.4673583
X-RAY DIFFRACTIONr_mcangle_it3.18252480
X-RAY DIFFRACTIONr_scbond_it4.3278814
X-RAY DIFFRACTIONr_scangle_it5.46411730
X-RAY DIFFRACTIONr_rigid_bond_restr1.90233825
X-RAY DIFFRACTIONr_sphericity_free10.2763456
X-RAY DIFFRACTIONr_sphericity_bonded4.00133747
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1074 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.75
LOOSE THERMAL2.0610
LS refinement shellResolution: 0.97→0.995 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 425 -
Rwork0.331 7737 -
all-8162 -
obs--98.03 %

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