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- PDB-3npp: Crystal structure of a Pfam DUF1093 family protein (BSU39620) fro... -

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Basic information

Entry
Database: PDB / ID: 3npp
TitleCrystal structure of a Pfam DUF1093 family protein (BSU39620) from Bacillus subtilis at 2.15 A resolution
ComponentsPfam DUF1093 family protein
KeywordsStructural Genomics / Unknown function / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyProtein of unknown function DUF1093 / Protein of unknown function DUF1093 / YxeA-like superfamily / Protein of unknown function (DUF1093) / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta / Uncharacterized protein YxeA
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Pfam DUF1093 family protein (BSU39620) from Bacillus subtilis at 2.15 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
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
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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_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: Pfam DUF1093 family protein
B: Pfam DUF1093 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,72818
Polymers20,2182
Non-polymers1,50916
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-76 kcal/mol
Surface area10690 Å2
MethodPISA
2
A: Pfam DUF1093 family protein
B: Pfam DUF1093 family protein
hetero molecules

A: Pfam DUF1093 family protein
B: Pfam DUF1093 family protein
hetero molecules

A: Pfam DUF1093 family protein
B: Pfam DUF1093 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,18354
Polymers60,6556
Non-polymers4,52848
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area23500 Å2
ΔGint-406 kcal/mol
Surface area22480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.535, 91.535, 59.130
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-210-

SO4

21A-210-

SO4

31A-299-

HOH

41B-288-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A0
2112B0
1214A30 - 39
2214B30 - 39
1312A40 - 50
2312B40 - 50
1414A51 - 98
2414B51 - 98
1512A99 - 115
2512B99 - 115

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Components

#1: Protein Pfam DUF1093 family protein / Uncharacterized protein yxeA


Mass: 10109.176 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yxeA, BSU39620, HS74A / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: P54940
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT (30-115) WAS EXPRESSED WITH THE PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THIS CONSTRUCT (30-115) WAS EXPRESSED WITH THE PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 3.54 Å3/Da / Density % sol: 65.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 3.200000000M (NH4)2SO4, 0.1M Bicine pH 9.0, 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
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 8, 2010 / Details: Flat mirror (vertical focusing)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91837 Å / Relative weight: 1
ReflectionResolution: 2.15→29.962 Å / Num. obs: 15880 / % possible obs: 100 % / Redundancy: 6.1 % / Biso Wilson estimate: 33.756 Å2 / Rsym value: 0.112

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0110refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
SCALA3.3.15data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.15→29.962 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.944 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 7.613 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.155
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 3. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 3. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 4. 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 5. GLYCEROL (GOL) AND SULFATE (SO4) FROM THE CRYSTALLIZATION/CRYOPROTECTANT SOLUTIONS HAVE BEEN MODELED INTO THE SOLVENT STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.217 791 5 %RANDOM
Rwork0.179 ---
obs0.181 15878 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 87.92 Å2 / Biso mean: 38.842 Å2 / Biso min: 18.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å2-0.22 Å20 Å2
2---0.44 Å20 Å2
3---0.66 Å2
Refinement stepCycle: LAST / Resolution: 2.15→29.962 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1392 0 87 117 1596
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221515
X-RAY DIFFRACTIONr_bond_other_d0.0050.021041
X-RAY DIFFRACTIONr_angle_refined_deg1.5371.9962037
X-RAY DIFFRACTIONr_angle_other_deg1.17232535
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.995178
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.31325.13574
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.63315254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.024156
X-RAY DIFFRACTIONr_chiral_restr0.0950.2198
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021630
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02297
X-RAY DIFFRACTIONr_mcbond_it0.7011.5869
X-RAY DIFFRACTIONr_mcbond_other0.2011.5359
X-RAY DIFFRACTIONr_mcangle_it1.3121396
X-RAY DIFFRACTIONr_scbond_it2.2843646
X-RAY DIFFRACTIONr_scangle_it3.5394.5638
Refine LS restraints NCS

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

NumberTypeRms dev position (Å)Weight position
166TIGHT POSITIONAL0.290.05
964MEDIUM POSITIONAL0.770.5
166TIGHT THERMAL0.80.5
964MEDIUM THERMAL1.32
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 58 -
Rwork0.228 1096 -
all-1154 -
obs--100 %
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)
13.68232.40232.46612.55371.51873.39430.14250.1531-0.2410.1659-0.0389-0.21890.33710.2714-0.10360.27890.03140.01360.2164-0.01750.078151.48816.014-5.45
21.59230.4584-0.50831.9464-0.95211.5142-0.02830.1013-0.2385-0.24380.02690.04920.212-0.01950.00140.2727-0.0015-0.01330.2066-0.04590.075341.76612.488-10.954
33.8794.7263.67464.5249-0.155324.97310.6522-0.4826-0.19430.708-0.5855-0.3106-0.0690.5298-0.06670.4092-0.0511-0.05890.34590.06050.267549.4110.5171.773
41.527-0.502-1.33361.5487-0.20789.31680.1776-0.31280.04920.6006-0.0649-0.12610.3470.0079-0.11260.4586-0.0826-0.03730.3878-0.00540.07859.56425.29816.922
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 46
2X-RAY DIFFRACTION2A47 - 115
3X-RAY DIFFRACTION3B0 - 37
4X-RAY DIFFRACTION4B38 - 115

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