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- PDB-3lwd: Crystal structure of Putative 6-phosphogluconolactonase (YP_57478... -

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Basic information

Entry
Database: PDB / ID: 3lwd
TitleCrystal structure of Putative 6-phosphogluconolactonase (YP_574786.1) from Chromohalobacter salexigens DSM 3043 at 1.88 A resolution
Components6-phosphogluconolactonase
KeywordsHYDROLASE / Putative 6-phosphogluconolactonase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


6-phosphogluconolactonase / 6-phosphogluconolactonase activity / pentose-phosphate shunt / carbohydrate metabolic process
Similarity search - Function
6-Phosphogluconolactonase / 6-phosphogluconolactonase, DevB-type / Glucosamine/galactosamine-6-phosphate isomerase / Glucosamine-6-phosphate isomerases/6-phosphogluconolactonase / Rossmann fold - #1360 / NagB/RpiA transferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
6-phosphogluconolactonase
Similarity search - Component
Biological speciesChromohalobacter salexigens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative 6-phosphogluconolactonase (YP_574786.1) from Chromohalobacter salexigens DSM 3043 at 1.88 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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.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 1.5Oct 9, 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: 6-phosphogluconolactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3784
Polymers24,1711
Non-polymers2073
Water4,468248
1
A: 6-phosphogluconolactonase
hetero molecules

A: 6-phosphogluconolactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7568
Polymers48,3412
Non-polymers4146
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area3580 Å2
ΔGint-36 kcal/mol
Surface area17470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.647, 60.647, 133.089
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein 6-phosphogluconolactonase


Mass: 24170.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromohalobacter salexigens (bacteria) / Strain: DSM 3043 / ATCC BAA-138 / NCIMB 13768 / Gene: Csal_2740 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q1QTX1, 6-phosphogluconolactonase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 248 / 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 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: 2.92 Å3/Da / Density % sol: 57.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10.0000% iso-Propanol, 20.0000% PEG-4000, 0.1M HEPES pH 7.5, 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: 0.91837,0.97937,0.97898
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 3, 2009 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979371
30.978981
ReflectionResolution: 1.75→48.84 Å / Num. obs: 65927 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.045 / Net I/σ(I): 14.49
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.75-1.950.4642.4187.8
1.95-2.030.3233.4196.6
2.03-2.120.2294.7196.8
2.12-2.230.1626.4197
2.23-2.370.1228.2197.2
2.37-2.550.0979.9197.3
2.55-2.810.06314.2197.6
2.81-3.210.03921.1197.8
3.21-4.040.02432197.9
4.04-48.840.01940197.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PHENIXrefinement
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.75→48.86 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 4.813 / SU ML: 0.066 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.09
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.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. 4.A SODIUM ION(NA) AND GLYCEROL (GOL) FROM CRYSTALLIZATION/CRYOPROTECTATION ARE MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.18628 1488 5.1 %RANDOM
Rwork0.15828 ---
obs0.15965 27822 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.63 Å2
Baniso -1Baniso -2Baniso -3
1-1.64 Å20.82 Å20 Å2
2--1.64 Å20 Å2
3----2.46 Å2
Refinement stepCycle: LAST / Resolution: 1.75→48.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1669 0 13 248 1930
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221846
X-RAY DIFFRACTIONr_bond_other_d0.0010.021240
X-RAY DIFFRACTIONr_angle_refined_deg1.1541.9732554
X-RAY DIFFRACTIONr_angle_other_deg0.77733045
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4455264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.05823.52985
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.6315295
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8241520
X-RAY DIFFRACTIONr_chiral_restr0.0830.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212132
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02368
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6581.51180
X-RAY DIFFRACTIONr_mcbond_other0.2061.5464
X-RAY DIFFRACTIONr_mcangle_it1.18321921
X-RAY DIFFRACTIONr_scbond_it1.9683666
X-RAY DIFFRACTIONr_scangle_it3.1954.5612
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 104 -
Rwork0.275 1996 -
obs--99.57 %
Refinement TLS params.Method: refined / Origin x: 8.6438 Å / Origin y: 23.7412 Å / Origin z: 51.6106 Å
111213212223313233
T0.0131 Å20.0127 Å20.0089 Å2-0.126 Å2-0.0149 Å2--0.0975 Å2
L1.6629 °2-0.0507 °20.9471 °2-1.1437 °2-0.5534 °2--3.1446 °2
S0.0158 Å °0.1751 Å °-0.0928 Å °-0.0784 Å °0.0569 Å °0.0982 Å °0.0728 Å °-0.094 Å °-0.0727 Å °

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