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- PDB-4zgf: Crystal structure of a duf4847 family protein (BVU_2626) from Bac... -

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Basic information

Entry
Database: PDB / ID: 4zgf
TitleCrystal structure of a duf4847 family protein (BVU_2626) from Bacteroides vulgatus ATCC 8482 at 1.00 A resolution
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


Protein of unknown function DUF4847 / Domain of unknown function (DUF4847) / HslJ-like superfamily / Lipocalin - #270 / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / BENZOIC ACID / DUF4847 domain-containing protein
Similarity search - Component
Biological speciesBacteroides vulgatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a duf4847 family protein (BVU_2626) from Bacteroides vulgatus ATCC 8482 at 1.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Advisory / Derived calculations ...Advisory / Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_struct_oper_list ...entity_src_gen / pdbx_struct_oper_list / pdbx_validate_symm_contact / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Feb 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
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_alt_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details
Revision 1.3Oct 23, 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: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,27311
Polymers15,7831
Non-polymers1,49010
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-19 kcal/mol
Surface area8800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.747, 55.486, 76.176
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Uncharacterized protein


Mass: 15783.202 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides vulgatus (bacteria) / Strain: ATCC 8482 / DSM 1447 / NCTC 11154 / Gene: BVU_2626 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A6L3L5

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Non-polymers , 5 types, 242 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE CONSTRUCT (25-164) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (25-164) 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: 2.13 Å3/Da / Density % sol: 42.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 40% polyethylene glycol 400, 0.2M calcium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.95369,0.97946,0.9793
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 12, 2015
Details: Vertical focusing mirror; double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.953691
20.979461
30.97931
ReflectionResolution: 1→29.304 Å / Num. obs: 72996 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 2.035 % / Biso Wilson estimate: 6.458 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.038 / Rrim(I) all: 0.05 / Net I/σ(I): 12.26 / Num. measured all: 281103
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) allDiffraction-ID% possible all
1-1.040.5090.6441.42805015574145450.851193.4
1.04-1.080.710.4182.22608213410133050.55199.2
1.08-1.130.8670.2523.52790814190140880.33399.3
1.13-1.190.9290.184.82768013975138380.23699
1.19-1.260.950.1485.82639113198130770.19599.1
1.26-1.360.9720.1117.72896814382141970.14698.7
1.36-1.490.9850.07810.52748313404132680.10399
1.49-1.710.9950.04716.52981514363142320.06299.1
1.71-2.150.9980.02627.92928314023138100.03498.5
2.150.9990.01542.42944314178137990.02197.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALENovember 3, 2014 BUILT=20141118data scaling
REFMAC5.8.0107refinement
SHELXDphasing
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1→29.304 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.977 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 0.632 / SU ML: 0.014 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.021 / ESU R Free: 0.022
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. 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 ...Details: 1. 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. 2. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 3. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 4. PEG (P6G), BEZ, CA AND ACT MODELED WERE PRESENT IN CRYSTALLIZATION/PROTEIN CONDITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.1365 3681 5 %RANDOM
Rwork0.116 69234 --
obs0.117 72915 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.01 Å2 / Biso mean: 12.2306 Å2 / Biso min: 4.99 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-0 Å2-0 Å2
2---0.05 Å20 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 1→29.304 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1114 0 84 232 1430
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191447
X-RAY DIFFRACTIONr_bond_other_d0.0020.021335
X-RAY DIFFRACTIONr_angle_refined_deg1.7211.9711963
X-RAY DIFFRACTIONr_angle_other_deg1.0133125
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2085187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.3126.19771
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.31515230
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.384153
X-RAY DIFFRACTIONr_chiral_restr0.1150.2193
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021723
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02336
X-RAY DIFFRACTIONr_mcbond_it0.6840.773680
X-RAY DIFFRACTIONr_mcbond_other0.6760.77677
X-RAY DIFFRACTIONr_mcangle_it0.8921.168879
X-RAY DIFFRACTIONr_rigid_bond_restr2.39932779
X-RAY DIFFRACTIONr_sphericity_free25.909541
X-RAY DIFFRACTIONr_sphericity_bonded7.06252946
LS refinement shellResolution: 1→1.027 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 240 -
Rwork0.274 4913 -
all-5153 -
obs--96.01 %

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