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- PDB-4qvu: Crystal structure of a DUF4931 family protein (BCE0241) from Baci... -

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Basic information

Entry
Database: PDB / ID: 4qvu
TitleCrystal structure of a DUF4931 family protein (BCE0241) from Bacillus cereus ATCC 10987 at 2.65 A resolution
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / HIT-like fold / PF16285 family / DUF4931 / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyGalactose-1-phosphate uridylyltransferase, short form, putative / Domain of unknown function (DUF4931) N-terminal domain / UDP-glucose:hexose-1-phosphate uridylyltransferase activity / Galactose-1-phosphate uridyl transferase, class I / galactose catabolic process via UDP-galactose / HIT-like superfamily / zinc ion binding / Uncharacterized protein
Function and homology information
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.65 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (BCE0241) from Bacillus cereus ATCC 10987 at 2.65 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Feb 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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

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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)31,3464
Polymers31,0641
Non-polymers2833
Water724
1
A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,38616
Polymers124,2554
Non-polymers1,13112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation11_655-x+y+1,y,-z1
Buried area11970 Å2
ΔGint-213 kcal/mol
Surface area34940 Å2
MethodPISA
2
A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6938
Polymers62,1282
Non-polymers5656
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area3390 Å2
ΔGint-112 kcal/mol
Surface area20060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.049, 102.049, 95.481
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein Uncharacterized protein


Mass: 31063.846 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 10987 / Gene: BCE_0241 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q73EW7
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE THE CONSTRUCT (RESIDUES 1-264) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. ...SEQUENCE THE CONSTRUCT (RESIDUES 1-264) 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: 2.31 Å3/Da / Density % sol: 46.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.47
Details: 53.00% polyethylene glycol 200, 0.1M HEPES pH 7.47, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9116,0.9794
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 27, 2014
Details: Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled 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
10.91161
20.97941
ReflectionResolution: 2.65→29.944 Å / Num. all: 8992 / Num. obs: 8992 / % possible obs: 99.9 % / Redundancy: 11.6 % / Biso Wilson estimate: 86.177 Å2 / Rsym value: 0.086 / Net I/σ(I): 16.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible allRmerge(I) obs
2.65-2.7212.42.380516481.267100
2.72-2.7912.40.977116210.8861000.013
2.79-2.8712.41.175036070.6791000.013
2.87-2.96121.572956060.51000.013
2.96-3.0611.61.967175770.3991000.013
3.06-3.1711.12.562885640.30799.90.013
3.17-3.2910.53.756655420.21000.013
3.29-3.4212.34.665115310.1631000.013
3.42-3.5712.25.360514940.1311000.013
3.57-3.7511.86.658084910.1011000.013
3.75-3.9511.77.654224650.0891000.013
3.95-4.1910.7946954400.071000.013
4.19-4.4811.310.146794140.0621000.013
4.48-4.8412.21048263950.061000.013
4.84-5.311.89.942703610.0631000.013
5.3-5.93119.837303390.0641000.013
5.93-6.849.99.829492980.0621000.013
6.84-8.3811.69.630042600.06399.90.013
8.38-11.859.911.221002130.05199.90.013
11.85-29.9449.29.111611260.05493.80.013

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
SCALA3.3.20data scaling
BUSTER-TNT2.10.0refinement
MOSFLMdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.65→29.944 Å / Cor.coef. Fo:Fc: 0.9372 / Cor.coef. Fo:Fc free: 0.9132 / Occupancy max: 1 / Occupancy min: 0.75 / 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. POLYETHYLENE GLYCOL 200 FRAGMENT (PG4) FROM THE CRYSTALLIZATION WERE MODELED INTO THE STRUCTURE. 5. THE MODELING OF ZINC (ZN) INTO THE STRUCTURE IS SUPPORTED BY ANOMALOUS DIFFERENCE DENSITY. 6. SODIUM (NA) FROM PURIFICATION BUFFER WAS MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.2607 556 6.2 %RANDOM
Rwork0.2068 ---
obs0.21 8971 99.96 %-
Displacement parametersBiso max: 166.27 Å2 / Biso mean: 83.7481 Å2 / Biso min: 46.96 Å2
Baniso -1Baniso -2Baniso -3
1--1.0758 Å20 Å20 Å2
2---1.0758 Å20 Å2
3---2.1516 Å2
Refine analyzeLuzzati coordinate error obs: 0.409 Å
Refinement stepCycle: LAST / Resolution: 2.65→29.944 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1715 0 9 4 1728
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d792SINUSOIDAL6
X-RAY DIFFRACTIONt_trig_c_planes44HARMONIC2
X-RAY DIFFRACTIONt_gen_planes253HARMONIC5
X-RAY DIFFRACTIONt_it1762HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC6
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion247SEMIHARMONIC5
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_contact1981SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1762HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg2398HARMONIC21.1
X-RAY DIFFRACTIONt_omega_torsion3.27
X-RAY DIFFRACTIONt_other_torsion2.18
LS refinement shellResolution: 2.65→2.96 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2347 160 6.48 %
Rwork0.2033 2310 -
all0.2054 2470 -
obs--99.96 %
Refinement TLS params.Method: refined / Origin x: 35.7484 Å / Origin y: 11.0894 Å / Origin z: 13 Å
111213212223313233
T-0.0562 Å2-0.0084 Å2-0.0058 Å2--0.1773 Å2-0.143 Å2---0.127 Å2
L2.421 °2-0.4871 °2-1.6994 °2-1.5742 °20.45 °2--3.7271 °2
S0.1046 Å °-0.2067 Å °0.2911 Å °0.1343 Å °-0.3472 Å °0.1788 Å °-0.3392 Å °-0.388 Å °0.2426 Å °

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