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- PDB-3iee: Crystal structure of an alpha helical protein (BF3319) from Bacte... -

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Basic information

Entry
Database: PDB / ID: 3iee
TitleCrystal structure of an alpha helical protein (BF3319) from Bacteroides fragilis NCTC 9343 at 1.70 A resolution
ComponentsPutative exported protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / YP_212931.1 / hypothetical protein BF3319 from Bacteroides fragilis / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Uncharacterised protein PF12889, C-terminal DUF3829 / : / DUF3829-like, C-terminal domain / Uncharacterised protein PF12889, N-terminal DUF3829 / : / Domain of unknown function (DUF6845) / Four Helix Bundle (Hemerythrin (Met), subunit A) / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesBacteroides fragilis NCTC 9343 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein BF3319 from Bacteroides fragilis (YP_212931.1) from Bacteroides fragilis NCTC 9343 at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 24, 2014Group: Structure summary
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jul 24, 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 1.5Feb 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: Putative exported protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2279
Polymers30,7311
Non-polymers4978
Water6,143341
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.525, 58.528, 94.125
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative exported protein


Mass: 30730.721 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis NCTC 9343 (bacteria)
Gene: BF3319, YP_212931.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q5LA60
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...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. THE CLONED CONSTRUCT CONTAINS RESIDUES 18-286 OF THE FULL LENGTH PROTEIN.

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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: 2.17 Å3/Da / Density % sol: 43.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 30.0000% PEG-6000, 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: BL9-2 / Wavelength: 0.97918
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 13, 2009 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.7→29.26 Å / Num. obs: 30021 / % possible obs: 99.4 % / Redundancy: 4.8 % / Biso Wilson estimate: 18.456 Å2 / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 11.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.744.40.661.2928120890.6696.1
1.74-1.794.80.5851.31033121360.58599.2
1.79-1.844.90.4591.71010420830.45999.5
1.84-1.94.90.3882973520000.38899.1
1.9-1.964.90.2952.6956619550.29599.2
1.96-2.034.90.233.4916018800.2399.4
2.03-2.114.90.1834.2897918410.18399.6
2.11-2.194.90.1495867817700.14999.9
2.19-2.294.90.1315.7829216950.13199.7
2.29-2.44.90.1176.2792716260.11799.8
2.4-2.534.80.1086.8761315700.10899.8
2.53-2.694.90.0987.4715014710.09899.9
2.69-2.874.80.0898676913970.08999.8
2.87-3.14.80.0828.2625412980.082100
3.1-3.44.80.0669.6579912070.066100
3.4-3.84.70.05710.9524411100.057100
3.8-4.394.70.05511.545819730.055100
4.39-5.384.60.05711.439128560.05799.9
5.38-7.64.40.0649.829326690.064100
7.6-29.263.90.04612.215543950.04698.1

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→29.26 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0.22 / SU B: 3.964 / SU ML: 0.068 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.1
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 RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. THE ETHYLENE GLYCOL (EDO) MOLECULES FROM THE CRYO SOLUTION WERE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.192 1517 5.1 %RANDOM
Rwork0.164 ---
obs0.166 29976 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.62 Å2 / Biso mean: 20.711 Å2 / Biso min: 6.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å20 Å20 Å2
2---0.32 Å20 Å2
3---0.93 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2029 0 32 341 2402
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222258
X-RAY DIFFRACTIONr_bond_other_d0.0040.021553
X-RAY DIFFRACTIONr_angle_refined_deg1.4651.9823059
X-RAY DIFFRACTIONr_angle_other_deg0.93533825
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9455292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.31525.446101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.68715429
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4831511
X-RAY DIFFRACTIONr_chiral_restr0.0860.2343
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022556
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02427
X-RAY DIFFRACTIONr_nbd_refined0.2380.2606
X-RAY DIFFRACTIONr_nbd_other0.1760.21657
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21186
X-RAY DIFFRACTIONr_nbtor_other0.0890.21066
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2265
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1040.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2580.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1650.234
X-RAY DIFFRACTIONr_mcbond_it2.11431449
X-RAY DIFFRACTIONr_mcbond_other0.6323549
X-RAY DIFFRACTIONr_mcangle_it2.60342283
X-RAY DIFFRACTIONr_scbond_it4.0335925
X-RAY DIFFRACTIONr_scangle_it5.6546776
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 106 -
Rwork0.226 1979 -
all-2085 -
obs--95.25 %
Refinement TLS params.Method: refined / Origin x: 7.0652 Å / Origin y: 40.6009 Å / Origin z: 10.6416 Å
111213212223313233
T-0.026 Å2-0.0089 Å2-0.0098 Å2--0.03 Å2-0.0029 Å2---0.0329 Å2
L0.5052 °20.0621 °20.0614 °2-0.3764 °20.077 °2--0.3806 °2
S0.0182 Å °0.0506 Å °-0.0249 Å °-0.0208 Å °0.0315 Å °-0.0146 Å °0.0268 Å °0.0103 Å °-0.0496 Å °

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