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Basic information

Entry
Database: PDB / ID: 3qkb
TitleCrystal structure of a Protein with unknown function which belongs to Pfam DUF74 family (PEPE_0654) from Pediococcus pentosaceus ATCC 25745 at 2.73 A resolution
ComponentsUncharacterized protein
KeywordsStructural Genomics / Unknown function / BETA/ALPHA-PROPELLER / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homologyUPF0145 domain superfamily / Hypothetical protein apc22750. Chain B / Translation Initiation Factor IF3 / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesPediococcus pentosaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.73 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Protein with unknown function which belongs to Pfam DUF74 family (PEPE_0654) from Pediococcus pentosaceus ATCC 25745 at 2.73 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJan 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name

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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
E: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)63,4295
Polymers63,4295
Non-polymers00
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10110 Å2
ΔGint-48 kcal/mol
Surface area18360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.296, 67.301, 85.836
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A0 - 90
2112B0 - 90
3112C0 - 90
4112D0 - 90
5112E0 - 90
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A PENTAMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein
Uncharacterized protein


Mass: 12685.804 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pediococcus pentosaceus (bacteria) / Strain: ATCC 25745 / 183-1w / Gene: PEPE_0654 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q03GF5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT (1-92) WAS EXPRESSED WITH THE PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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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: 2.51 Å3/Da / Density % sol: 51.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 30.00% MPD, 0.200M NH4OAc, 0.1M Citrate pH 5.6, 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: 0.91162,0.97929
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 8, 2009 / 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
10.911621
20.979291
ReflectionResolution: 2.73→47.727 Å / Num. obs: 17422 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 60.247 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.92
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.73-2.830.7572.165301768199.3
2.83-2.940.5162.961461667199.3
2.94-3.070.4083.561481674199.3
3.07-3.230.2725.162921707199.1
3.23-3.440.1857.165561782199.3
3.44-3.70.1359.362451704199.1
3.7-4.070.08613.563171737199.3
4.07-4.650.05418.863091738199.1
4.65-5.840.0520.564231781198.7
5.84-47.7270.04424.864901864195.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEdata scaling
REFMAC5.5.0110refinement
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.73→47.727 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.916 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 24.741 / SU ML: 0.238 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.782 / ESU R Free: 0.314
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 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.2393 884 5.1 %RANDOM
Rwork0.2018 ---
obs0.2037 17408 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 127.2 Å2 / Biso mean: 54.0681 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å20 Å2
2---0.27 Å20 Å2
3---0.75 Å2
Refinement stepCycle: LAST / Resolution: 2.73→47.727 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3543 0 0 54 3597
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223660
X-RAY DIFFRACTIONr_bond_other_d0.0040.022365
X-RAY DIFFRACTIONr_angle_refined_deg1.2951.9784954
X-RAY DIFFRACTIONr_angle_other_deg1.10735895
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7275483
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.19527.115156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.25815678
X-RAY DIFFRACTIONr_chiral_restr0.0690.2585
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024076
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02656
X-RAY DIFFRACTIONr_mcbond_it0.6051.52311
X-RAY DIFFRACTIONr_mcbond_other0.1021.5975
X-RAY DIFFRACTIONr_mcangle_it1.15123724
X-RAY DIFFRACTIONr_scbond_it1.49231349
X-RAY DIFFRACTIONr_scangle_it2.3554.51218
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A517TIGHT POSITIONAL0.030.05
B517TIGHT POSITIONAL0.030.05
C517TIGHT POSITIONAL0.040.05
D517TIGHT POSITIONAL0.040.05
E517TIGHT POSITIONAL0.040.05
A531MEDIUM POSITIONAL0.030.5
B531MEDIUM POSITIONAL0.040.5
C531MEDIUM POSITIONAL0.040.5
D531MEDIUM POSITIONAL0.040.5
E531MEDIUM POSITIONAL0.040.5
A517TIGHT THERMAL0.070.5
B517TIGHT THERMAL0.070.5
C517TIGHT THERMAL0.090.5
D517TIGHT THERMAL0.080.5
E517TIGHT THERMAL0.080.5
A531MEDIUM THERMAL0.072
B531MEDIUM THERMAL0.162
C531MEDIUM THERMAL0.092
D531MEDIUM THERMAL0.112
E531MEDIUM THERMAL0.122
LS refinement shellResolution: 2.73→2.801 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.428 62 -
Rwork0.331 1228 -
all-1290 -
obs--99.23 %
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)
11.95350.68790.06944.93592.27655.4314-0.08680.68340.4259-0.6484-0.02660.1516-0.4792-0.16380.11340.4775-0.0279-0.05510.29310.14810.333732.6833.09856.598
22.46071.60890.58989.93754.45794.302-0.15330.55950.1949-0.59360.1511-0.4557-0.08160.24660.00220.3474-0.04630.05680.19330.04690.260243.42421.93161.192
33.41542.49111.1965.10110.88223.3571-0.14310.3484-0.1127-0.1630.1057-0.19210.08160.32440.03740.2419-0.01770.05520.0573-0.00940.261636.54812.82172.65
42.87331.12370.9193.66722.00444.1196-0.10420.1214-0.05860.1527-0.06590.7240.1278-0.36760.170.2553-0.04630.05640.0531-0.00460.472421.52118.38375.031
50.9969-0.1270.89142.84852.29068.3142-0.10260.32740.1079-0.18780.00550.5861-0.2766-0.61650.09710.3501-0.019-0.08950.28250.07450.539419.6130.89965.951
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 92
2X-RAY DIFFRACTION2B-1 - 92
3X-RAY DIFFRACTION3C0 - 92
4X-RAY DIFFRACTION4D-1 - 92
5X-RAY DIFFRACTION5E0 - 91

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