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- PDB-4e6f: Crystal structure of a DUF4468 family protein (BACOVA_04320) from... -

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Basic information

Entry
Database: PDB / ID: 4e6f
TitleCrystal structure of a DUF4468 family protein (BACOVA_04320) from Bacteroides ovatus ATCC 8483 at 1.49 A resolution
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / PF14730 FAMILY PROTEIN / DUF4468 WITH TBP-LIKE FOLD / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homologyAlpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 - #80 / Domain of unknown function DUF4468 with TBP-like fold / Domain of unknown function (DUF4468) with TBP-like fold / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / 2-Layer Sandwich / Alpha Beta / NITRATE ION / DUF4468 domain-containing protein
Function and homology information
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.49 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (BACOVA_04320) from Bacteroides ovatus ATCC 8483 at 1.49 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _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: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,48812
Polymers41,8682
Non-polymers62010
Water12,989721
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1825
Polymers20,9341
Non-polymers2484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3067
Polymers20,9341
Non-polymers3726
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.237, 89.078, 52.586
Angle α, β, γ (deg.)90.000, 105.490, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uncharacterized protein


Mass: 20934.107 Da / Num. of mol.: 2 / Fragment: UNP residues 25-384
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus (bacteria) / Gene: BACOVA_04320 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7M2I6
#2: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 721 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE UNIT CELL IS TOO SMALL TO CONTAIN THE INTACT PURIFIED PROTEIN CONSTRUCT RESIDUES 25-384). ...THE UNIT CELL IS TOO SMALL TO CONTAIN THE INTACT PURIFIED PROTEIN CONSTRUCT RESIDUES 25-384). THEREFORE, THE CRYSTAL MUST CONTAIN A PROTEOLYTIC FRAGMENT. THE PROTEOLTIC BOUNDARY IS NOT KNOWN. RESIDUES 30-200 WERE MODELED IN CHAIN A AND 32-204 IN CHAIN B BASED ON THE ELECTRON DENSITY.
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 25-384 OF THE TARGET SEQUENCE. AFTER PURIFICATION, THE INTACT CONSTRUCT WAS CONFIRMED VIA MASS SPECTROMETRY WITH NO EVIDENCE OF PROTEOYLSIS IN THE SDS-GEL. HOWEVER, SINCE THERE IS EVIDENCE OF PROTEOLYSIS IN THE CRYSTAL STRUCTURE AND THE BOUNDARY IS NOT KNOWN, THE SEQRES RECORDS REFLECT THE RESIDUES OBSERVED IN THE ELECTRON DENSITY MAP.

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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: 2.65 Å3/Da / Density % sol: 53.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.20M potassium nitrate, 20.00% polyethylene glycol 3350, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97972,0.91837,0.97917
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2012
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979721
20.918371
30.979171
ReflectionResolution: 1.49→47.449 Å / Num. obs: 69985 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 3.42 % / Biso Wilson estimate: 17.175 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 12.94
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.49-1.543.360.5462.1922139659498
1.54-1.60.3972.821899678197.8
1.6-1.680.3133.827123772298.8
1.68-1.770.2185.324582709698.4
1.77-1.880.157.322449682297.3
1.88-2.020.09911.123812675398.5
2.02-2.230.06615.825322726698.8
2.23-2.550.05319.623414687197.5
2.55-3.210.04126.124672702998.9
3.21-47.4490.0283523721705197

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEDecember 29, 2011data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 1.49→47.449 Å / Cor.coef. Fo:Fc: 0.9677 / Cor.coef. Fo:Fc free: 0.9604 / Occupancy max: 1 / Occupancy min: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0
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. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 4. NITRATE AND ETHYLENE GLYCOL MODELED WERE PRESENT IN CRYSTALLIZATION CONDITION OR CRYOPROTECTANT. 5. THE C-TERMINAL PORTION OF THE PROTEIN WAS PRESENT AFTER PURIFICATION, BUT IS NOT OBSERVED IN THE CRYSTAL STRUCTURE. THE SIZE OF THE UNIT CELL IS TOO SMALL TO CONTAIN THE FULL CONSTRUCT. THEREFORE THE CRYSTAL MUST CONTAIN A PROTEOLYTIC FRAGMENT. HOWEVER, THE SITE OF PROTEOLYSIS IS UNKNOWN. RESIDUES 30-200 WERE MODELED IN CHAIN A AND 32-204 IN CHAIN B.
RfactorNum. reflection% reflectionSelection details
Rfree0.18 3538 5.06 %RANDOM
Rwork0.1604 ---
obs0.1614 69962 98.22 %-
Displacement parametersBiso max: 106.26 Å2 / Biso mean: 24.53 Å2 / Biso min: 7.17 Å2
Baniso -1Baniso -2Baniso -3
1--1.4924 Å20 Å2-0.0089 Å2
2--0.6714 Å20 Å2
3---0.8209 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 1.49→47.449 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2748 0 40 721 3509
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1501SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes81HARMONIC2
X-RAY DIFFRACTIONt_gen_planes471HARMONIC5
X-RAY DIFFRACTIONt_it3058HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion412SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4196SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3058HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4169HARMONIC20.97
X-RAY DIFFRACTIONt_omega_torsion4.05
X-RAY DIFFRACTIONt_other_torsion2.67
LS refinement shellResolution: 1.49→1.53 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2328 264 5.14 %
Rwork0.2072 4868 -
all0.2085 5132 -
obs--98.22 %
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)
10.4672-0.5221-0.02661.00720.07781.50870.0615-0.03380.08460.0686-0.0066-0.1329-0.1650.0239-0.0550.0077-0.0264-0.005-0.0814-0.002-0.047332.511419.158116.7429
21.27650.1883-0.17050.8158-0.16620.57330-0.06830.0192-0.0145-0.02580.01790.1120.01880.0258-0.01880.0037-0.0084-0.04460.0007-0.041815.019933.7584-3.8164
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 200
2X-RAY DIFFRACTION2B32 - 204

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