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- PDB-4qrj: Crystal structure of a putative 6-phosphogluconolactonase (BACUNI... -

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Basic information

Entry
Database: PDB / ID: 4qrj
TitleCrystal structure of a putative 6-phosphogluconolactonase (BACUNI_04672) from Bacteroides uniformis ATCC 8492 at 2.20 A resolution
Componentsputative 6-phosphogluconolactonase
KeywordsHYDROLASE / Lactonase / PF10282 family protein / 7-bladed beta-propeller / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


: / Lactonase, 7-bladed beta propeller / Lactonase, 7-bladed beta-propeller / Cytochrome cd1-nitrite reductase-like, haem d1 domain superfamily / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Prokaryotic membrane lipoprotein lipid attachment site profile. / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / Lactonase family protein
Similarity search - Component
Biological speciesBacteroides uniformis ATCC 8492 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative 6-phosphogluconolactonase (BACUNI_04672) from Bacteroides uniformis ATCC 8492 at 2.20 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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
Revision 1.4Oct 30, 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

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Assembly

Deposited unit
A: putative 6-phosphogluconolactonase
B: putative 6-phosphogluconolactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,9097
Polymers76,4252
Non-polymers4845
Water3,837213
1
A: putative 6-phosphogluconolactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5905
Polymers38,2131
Non-polymers3774
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: putative 6-phosphogluconolactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3192
Polymers38,2131
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.554, 52.185, 78.880
Angle α, β, γ (deg.)95.220, 90.540, 94.370
Int Tables number1
Space group name H-MP1

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Components

#1: Protein putative 6-phosphogluconolactonase


Mass: 38212.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides uniformis ATCC 8492 (bacteria)
Gene: BACUNI_04672, ZP_02073211.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7VAP0
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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 RESIDUES 24-370 OF 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: 2.17 Å3/Da / Density % sol: 43.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M sodium acetate, 30.0% polyethylene glycol 4000, 0.1M tris hydrochloride pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97925
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 22, 2013
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 2.2→29.302 Å / Num. obs: 29206 / % possible obs: 87.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 33.147 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 6.68
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.2-2.280.2232.26783558384.1
2.28-2.370.1962.56622545284.3
2.37-2.480.1682.87149586989.3
2.48-2.610.1323.66977571688.2
2.61-2.770.1134.46636547185.6
2.77-2.980.0935.86742556087
2.98-3.280.0677.97245600190.7
3.28-3.760.04910.66739557784.4
3.76-4.720.04113.16998581190.5
4.720.03813.66959576887.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
PHASERphasing
XSCALEJuly 4, 2012data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→29.302 Å / Cor.coef. Fo:Fc: 0.9485 / Cor.coef. Fo:Fc free: 0.9346 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION ...Details: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3.NCS RESTRAINTS WERE IMPOSED BY AUTOBUSTER'S LSSR PROCEDURE (-AUTONCS)
RfactorNum. reflection% reflectionSelection details
Rfree0.1925 1467 5.02 %RANDOM
Rwork0.1573 ---
obs0.1591 29203 89.62 %-
Displacement parametersBiso max: 117.97 Å2 / Biso mean: 36.3736 Å2 / Biso min: 9.27 Å2
Baniso -1Baniso -2Baniso -3
1--0.2633 Å24.659 Å20.0999 Å2
2---6.7911 Å22.8086 Å2
3---7.0544 Å2
Refine analyzeLuzzati coordinate error obs: 0.261 Å
Refinement stepCycle: LAST / Resolution: 2.2→29.302 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5213 0 32 213 5458
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2433SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes134HARMONIC2
X-RAY DIFFRACTIONt_gen_planes806HARMONIC5
X-RAY DIFFRACTIONt_it5404HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion733SEMIHARMONIC5
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_contact6432SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5404HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg7368HARMONIC21.07
X-RAY DIFFRACTIONt_omega_torsion3.87
X-RAY DIFFRACTIONt_other_torsion2.67
LS refinement shellResolution: 2.2→2.28 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2328 121 4.28 %
Rwork0.1747 2703 -
all0.1771 2824 -
obs--89.62 %
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)
11.15530.52060.02271.1379-0.03772.2910.0096-0.0542-0.1459-0.0289-0.00240.01940.3423-0.1069-0.0072-0.0995-0.00950.0118-0.0803-0.0117-0.091920.072311.156526.9129
21.05750.40730.22481.0947-0.08552.0862-0.0290.05210.15390.00540.0421-0.0435-0.30510.0595-0.0132-0.0997-0.01710.014-0.0692-0.0238-0.081227.917628.206968.1675
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|26-370 }A26 - 370
2X-RAY DIFFRACTION2{ B|26-370 }B26 - 370

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