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- PDB-3scy: Crystal structure of a putative 6-phosphogluconolactonase (BF1038... -

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Basic information

Entry
Database: PDB / ID: 3scy
TitleCrystal structure of a putative 6-phosphogluconolactonase (BF1038) from Bacteroides fragilis NCTC 9343 at 1.50 A resolution
ComponentsHypothetical bacterial 6-phosphogluconolactonase
KeywordsHYDROLASE / 7-bladed beta-propeller / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


6-phosphogluconolactonase activity / cytosol
Similarity search - Function
: / 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
Unknown ligand / Uncharacterized protein
Similarity search - Component
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Hypothetical bacterial 6-phosphogluconolactonase (BF1038) from Bacteroides fragilis NCTC 9343 at 1.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
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_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_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_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 1.4Nov 27, 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: Hypothetical bacterial 6-phosphogluconolactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3655
Polymers39,2931
Non-polymers724
Water6,413356
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.463, 49.463, 216.435
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Hypothetical bacterial 6-phosphogluconolactonase


Mass: 39293.371 Da / Num. of mol.: 1 / Fragment: sequence database residues 25-384
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: ATCC 25285 / NCTC 9343 / Gene: BF1038 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q5LGG4
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#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.: 356 / 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 25-384 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: 1.95 Å3/Da / Density % sol: 36.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30.00% polyethylene glycol 4000, 0.20M magnesium chloride, 0.1M TRIS pH 8.5, 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: 0.91837,0.97927
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
10.918371
20.979271
ReflectionResolution: 1.5→27.054 Å / Num. obs: 50531 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 21.616 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 17.52
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.5-1.550.6382326178811199.5
1.55-1.620.4442.93994210615199.9
1.62-1.690.314.2338648962199.9
1.69-1.780.2046.2363609564199.9
1.78-1.890.1239.9354269318199.9
1.89-2.040.07316.2371039742199.9
2.04-2.240.0523.2348269240199.9
2.24-2.560.03928.9349989326199.8
2.56-3.230.02937.2354389583199.7
3.23-27.0540.0244.6349809442198.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEDecember 6, 2010data scaling
BUSTER-TNT2.8.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MAD / Resolution: 1.5→27.054 Å / Cor.coef. Fo:Fc: 0.9654 / Cor.coef. Fo:Fc free: 0.9602 / 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. MAGNESIUM (MG) AND SODIUM (NA) FROM THE CRYSTALLIZATION AND PURIFICATIONS SOLUTIONS RESPECTIVELY HAVE BEEN MODELED INTO THE STRUCTURE. 4. AN UNNOWN LIGAND (UNL) HAS BEEN MODELED INTO THE PUTATIVE ACTIVE SITE. 5. THE REFINEMENT WAS RESTRAINED AGAINST THE MAD PHASES.
RfactorNum. reflection% reflectionSelection details
Rfree0.1855 2559 5.07 %RANDOM
Rwork0.1641 ---
obs0.1652 50438 --
Displacement parametersBiso max: 100.58 Å2 / Biso mean: 28.6549 Å2 / Biso min: 13.1 Å2
Baniso -1Baniso -2Baniso -3
1--2.2975 Å20 Å20 Å2
2---2.2975 Å20 Å2
3---4.5951 Å2
Refinement stepCycle: LAST / Resolution: 1.5→27.054 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2693 0 9 356 3058
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1352SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes75HARMONIC2
X-RAY DIFFRACTIONt_gen_planes443HARMONIC5
X-RAY DIFFRACTIONt_it2868HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion400SEMIHARMONIC5
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_contact3661SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2868HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3926HARMONIC21.11
X-RAY DIFFRACTIONt_omega_torsion4.55
X-RAY DIFFRACTIONt_other_torsion2.49
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2402 172 4.77 %
Rwork0.2129 3436 -
all0.2141 3608 -
Refinement TLS params.Method: refined / Origin x: -7.6948 Å / Origin y: 29.625 Å / Origin z: 16.3729 Å
111213212223313233
T-0.0347 Å20.0205 Å20.0186 Å2--0.0963 Å2-0.0054 Å2---0.0705 Å2
L0.8451 °20.0212 °2-0.2988 °2-0.529 °20.5697 °2--2.2436 °2
S0.0421 Å °-0.0166 Å °-0.0465 Å °0.035 Å °-0.0795 Å °0.0155 Å °-0.0123 Å °0.0108 Å °0.0375 Å °
Refinement TLS groupSelection details: chain A

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