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- PDB-3css: Crystal structure of 6-phosphogluconolactonase from Leishmania gu... -

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Basic information

Entry
Database: PDB / ID: 3css
TitleCrystal structure of 6-phosphogluconolactonase from Leishmania guyanensis
Components6-phosphogluconolactonase
KeywordsHYDROLASE / STRUCTURAL GENOMICS / Medical Structural Genomics of Pathogenic Protozoa Consortium / SGPP / 6-phosphogluconolactonase / leishmaniasis / PSI-2 / Protein Structure Initiative
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
PHOSPHATE ION / 6-phosphogluconolactonase
Similarity search - Component
Biological speciesLeishmania braziliensis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 Å
AuthorsArakaki, T.L. / Merritt, E.A. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2006
Title: Optimal description of a protein structure in terms of multiple groups undergoing TLS motion.
Authors: Painter, J. / Merritt, E.A.
History
DepositionApr 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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: 6-phosphogluconolactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7842
Polymers28,6891
Non-polymers951
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.999, 89.381, 100.521
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein 6-phosphogluconolactonase


Mass: 28688.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania braziliensis (eukaryote) / Strain: MHOM/BR/75/M2904 / Gene: LbrM26_V2.2630, LbrM26_V2.2660 / Plasmid: BG1861 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A4HFB4, gluconolactonase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THE DIFFERENCES IN THE SEQUENCE ARE DUE TO STRAIN VARIATIONS.

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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: 2.74 Å3/Da / Density % sol: 55.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 40% PEG 400, 0.1 M Sodium acetate, 0.1 M NH4H2PO4 pH 5.0, pH 7.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 3, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 33580 / % possible obs: 95.8 % / Redundancy: 7 % / Rmerge(I) obs: 0.04 / Χ2: 1.07 / Net I/σ(I): 14.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.7-1.764.40.40925031.014172.9
1.76-1.836.20.35230440.981187
1.83-1.916.80.26233531.053197.9
1.91-2.027.30.18834801.121199.9
2.02-2.147.50.12434791.1121100
2.14-2.317.50.08534971.1871100
2.31-2.547.50.06634881.2421100
2.54-2.917.50.04435180.9751100
2.91-3.667.50.03435481.0681100
3.66-507.20.02136700.884199.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
MAR345CCDdata collection
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 3CH7

3ch7


Resolution: 1.7→40 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.339 / SU ML: 0.057 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.185 1693 5 %RANDOM
Rwork0.169 ---
obs0.17 33570 95.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.359 Å2
Baniso -1Baniso -2Baniso -3
1--1.14 Å20 Å20 Å2
2--1.84 Å20 Å2
3----0.7 Å2
Refinement stepCycle: LAST / Resolution: 1.7→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1991 0 5 202 2198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222136
X-RAY DIFFRACTIONr_bond_other_d0.0010.021457
X-RAY DIFFRACTIONr_angle_refined_deg1.31.9862923
X-RAY DIFFRACTIONr_angle_other_deg0.89633598
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.085293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.8524.30286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.14815382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9151515
X-RAY DIFFRACTIONr_chiral_restr0.0720.2346
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212394
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02402
X-RAY DIFFRACTIONr_mcbond_it0.6151.51366
X-RAY DIFFRACTIONr_mcbond_other0.1631.5545
X-RAY DIFFRACTIONr_mcangle_it1.09522227
X-RAY DIFFRACTIONr_scbond_it1.743770
X-RAY DIFFRACTIONr_scangle_it2.7654.5682
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 90 -
Rwork0.276 1709 -
all-1799 -
obs--70.72 %
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)
14.8175-0.4239-0.30881.5747-0.49833.03180.03630.4291-0.2153-0.09050.09550.00430.35170.5268-0.13180.06720.0378-0.00040.0616-0.00290.026232.324122.336637.1272
24.40090.31110.11030.50830.67373.82760.00140.3494-0.4007-0.0317-0.10290.00590.5374-0.17330.10150.0934-0.04510.01430.0852-0.04980.015621.090519.722128.6813
33.7574-2.7146-2.5493.88081.8024.06730.29260.76730.1777-0.6475-0.38680.0077-0.6453-0.31370.09420.04980.043-0.04910.19490.0757-0.062815.849237.775426.2804
41.7557-0.304-0.27223.96960.49664.50970.14340.6953-0.0291-0.2024-0.25990.03630.1373-0.6050.1166-0.0206-0.0398-0.03670.2932-0.0512-0.098716.085125.368222.861
54.9111.4636-0.32729.88062.4243.8921-0.03590.63220.506-0.3432-0.03830.5061-0.5195-0.57010.0742-0.00660.0948-0.11240.25810.12250.00747.064343.994729.9519
60.86850.5994-0.3716.8559-0.61531.9292-0.11070.31080.1215-0.06330.00590.37660.0754-0.69750.1047-0.118-0.0268-0.0410.2284-0.01680.02154.148432.501436.6572
79.20750.9285-8.13030.0953-0.749610.0952-0.1844-0.0968-0.17320.02590.1382-0.0056-0.02960.18770.04620.0729-0.09010.02850.13480.02120.05484.487122.818148.4179
81.10970.23650.16891.70930.28161.3173-0.037-0.00740.12050.0144-0.02730.1245-0.0509-0.25830.06440.01180-0.00530.09080.00450.037916.030536.602741.9061
90.5832-0.23810.18881.99260.44341.9252-0.0298-0.0317-0.00270.16020.0672-0.1540.081-0.0286-0.03740.04280.0061-0.01660.080.01250.060628.320532.212547.969
106.1072-4.78515.94168.113-8.266815.0522-0.2751-0.41270.28840.45170.2398-0.8045-0.13150.38880.0353-0.04340.0083-0.04670.1377-0.05630.11340.257431.706446.1391
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 294 - 29
2X-RAY DIFFRACTION2AA30 - 7330 - 73
3X-RAY DIFFRACTION3AA74 - 8974 - 89
4X-RAY DIFFRACTION4AA90 - 10690 - 106
5X-RAY DIFFRACTION5AA107 - 120107 - 120
6X-RAY DIFFRACTION6AA121 - 143121 - 143
7X-RAY DIFFRACTION7AA144 - 155144 - 155
8X-RAY DIFFRACTION8AA156 - 212156 - 212
9X-RAY DIFFRACTION9AA213 - 258213 - 258
10X-RAY DIFFRACTION10AA259 - 267259 - 267

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