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- PDB-3s9j: Crystal structure of a member of duf4221 family (BVU_1028) from B... -

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Basic information

Entry
Database: PDB / ID: 3s9j
TitleCrystal structure of a member of duf4221 family (BVU_1028) from Bacteroides vulgatus atcc 8482 at 1.75 A resolution
ComponentsMember of DUF4221 family
KeywordsUNKNOWN FUNCTION / 6-bladed beta-propeller / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyProtein of unknown function DUF4221 / Domain of unknown function (DUF4221) / Prokaryotic membrane lipoprotein lipid attachment site profile. / FORMIC ACID / DUF4221 domain-containing protein
Function and homology information
Biological speciesBacteroides vulgatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Member of DUF4221 family (BVU_1028) from Bacteroides vulgatus ATCC 8482 at 1.75 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 23, 2011Group: Structure summary
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Member of DUF4221 family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,58220
Polymers43,6381
Non-polymers94419
Water8,431468
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)113.551, 113.551, 77.697
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-767-

HOH

DetailsCRYSTAL PACKING ANALYSIS SUGGEST THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION

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Components

#1: Protein Member of DUF4221 family


Mass: 43637.973 Da / Num. of mol.: 1 / Fragment: sequence database residues 27-394
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides vulgatus (bacteria) / Strain: ATCC 8482 / DSM 1447 / NCTC 11154 / Gene: BVU_1028 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6KZ57
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 468 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT (RESIDUES 27-394) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 27-394) WAS EXPRESSED WITH A 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: 3.31 Å3/Da / Density % sol: 62.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10.00% Glycerol, 3.60M sodium formate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162,0.97925
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 22, 2011 / Details: double crystal monochromator
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979251
ReflectionResolution: 1.75→28.388 Å / Num. all: 57440 / Num. obs: 57440 / % possible obs: 99.9 % / Redundancy: 4.5 % / Biso Wilson estimate: 24.618 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 10.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.75-1.84.40.5951.31860341880.59599.9
1.8-1.844.40.4851.61838941400.48599.9
1.84-1.94.40.37721782340100.37799.9
1.9-1.964.50.2891.71743239130.289100
1.96-2.024.50.2213.41683737650.221100
2.02-2.094.50.1823.61636636720.182100
2.09-2.174.50.1385.31565535060.138100
2.17-2.264.50.12161522934030.121100
2.26-2.364.50.116.31461832680.11100
2.36-2.474.50.1125.91395231150.112100
2.47-2.614.50.1066.31340629870.106100
2.61-2.774.50.0976.81251227990.097100
2.77-2.964.50.0837.51188526520.083100
2.96-3.24.50.0728.51102324610.072100
3.2-3.54.50.06191019522680.061100
3.5-3.914.50.05410.7925020660.054100
3.91-4.524.50.05511.2807918110.05599.9
4.52-5.534.40.05211690915530.052100
5.53-7.834.40.05312525412000.053100
7.83-28.3884.10.05411.727076630.05496.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
SCALA3.3.15data scaling
REFMAC5.5.0110refinement
MOSFLMdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.75→28.388 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.971 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 3.271 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.078 / ESU R Free: 0.079
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 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. 5.SODIUM (NA), FORMATE (FMT) AND GLYCEROL (GOL) FROM THE CRYSTALLIZATION CONDITION HAVE BEEN MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.1686 2913 5.1 %RANDOM
Rwork0.1423 ---
obs0.1436 57423 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 83.59 Å2 / Biso mean: 33.9517 Å2 / Biso min: 13.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20.35 Å20 Å2
2--0.7 Å20 Å2
3----1.04 Å2
Refinement stepCycle: LAST / Resolution: 1.75→28.388 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3003 0 60 468 3531
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223387
X-RAY DIFFRACTIONr_bond_other_d0.0020.022419
X-RAY DIFFRACTIONr_angle_refined_deg1.4751.974604
X-RAY DIFFRACTIONr_angle_other_deg0.89235916
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4075429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.28824.389180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.25315614
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0491518
X-RAY DIFFRACTIONr_chiral_restr0.0910.2466
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213780
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02730
X-RAY DIFFRACTIONr_mcbond_it1.60531951
X-RAY DIFFRACTIONr_mcbond_other0.4583771
X-RAY DIFFRACTIONr_mcangle_it2.64853161
X-RAY DIFFRACTIONr_scbond_it4.11881436
X-RAY DIFFRACTIONr_scangle_it6.122111405
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 217 -
Rwork0.219 3963 -
all-4180 -
obs--99.9 %
Refinement TLS params.Method: refined / Origin x: 32.9036 Å / Origin y: 32.7871 Å / Origin z: 27.7335 Å
111213212223313233
T0.0365 Å20.0059 Å20.0144 Å2-0.0644 Å2-0.0106 Å2--0.0664 Å2
L0.6492 °2-0.4036 °2-0.0374 °2-1.1289 °20.015 °2--0.8146 °2
S-0.056 Å °-0.0335 Å °-0.1142 Å °0.0436 Å °0.0068 Å °0.1509 Å °0.1234 Å °-0.134 Å °0.0491 Å °

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