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- PDB-3etn: Crystal structure of putative phosphosugar isomerase involved in ... -

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Basic information

Entry
Database: PDB / ID: 3etn
TitleCrystal structure of putative phosphosugar isomerase involved in capsule formation (YP_209877.1) from Bacteroides fragilis NCTC 9343 at 1.70 A resolution
Componentsputative phosphosugar isomerase involved in capsule formation
KeywordsISOMERASE / YP_209877.1 / putative phosphosugar isomerase involved in capsule formation / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Unknown function
Function / homology
Function and homology information


carbohydrate derivative metabolic process / carbohydrate derivative binding / isomerase activity
Similarity search - Function
KpsF-like, SIS domain / SIS domain / SIS domain / SIS domain profile. / Glucose-6-phosphate isomerase like protein; domain 1 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-CMK / Putative sugar isomerase SIS-domain protein
Similarity search - Component
Biological speciesBacteroides fragilis NCTC 9343 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structural analysis of arabinose-5-phosphate isomerase from Bacteroides fragilis and functional implications.
Authors: Chiu, H.J. / Grant, J.C. / Farr, C.L. / Jaroszewski, L. / Knuth, M.W. / Miller, M.D. / Elsliger, M.A. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A.
History
DepositionOct 8, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 5, 2014Group: Database references
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jul 24, 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 1.5Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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: putative phosphosugar isomerase involved in capsule formation
B: putative phosphosugar isomerase involved in capsule formation
C: putative phosphosugar isomerase involved in capsule formation
D: putative phosphosugar isomerase involved in capsule formation
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,64017
Polymers97,9084
Non-polymers2,73213
Water13,061725
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21310 Å2
ΔGint-103 kcal/mol
Surface area24850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.409, 114.267, 115.917
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA0 - 1730 - 173
21BB0 - 1730 - 173
31CC0 - 1730 - 173
41DD0 - 1730 - 173
12AA175 - 191175 - 191
22BB175 - 191175 - 191
32CC175 - 191175 - 191
42DD175 - 191175 - 191

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Components

#1: Protein
putative phosphosugar isomerase involved in capsule formation / Putative sugar isomerase SIS-domain protein


Mass: 24476.986 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis NCTC 9343 (bacteria)
Gene: YP_209877.1, BF0137 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q5LIW1
#2: Chemical
ChemComp-CMK / CYTIDINE 5'-MONOPHOSPHATE 3-DEOXY-BETA-D-GULO-OCT-2-ULO-PYRANOSONIC ACID / CMP-2-KETO-3-DEOXY-OCTULOSONIC ACID


Mass: 543.373 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H26N3O15P
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 725 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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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: 2.04 Å3/Da / Density % sol: 39.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 5.0% PEG-6000, 0.1M MES pH 6.0, 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: 0.91837,0.97910,0.97849
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 1, 2008 / 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
20.97911
30.978491
ReflectionResolution: 1.7→29.223 Å / Num. obs: 88793 / % possible obs: 99.8 % / Redundancy: 4.5 % / Biso Wilson estimate: 19.097 Å2 / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Net I/σ(I): 5.554
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.744.50.8190.92902364710.819100
1.74-1.794.50.6621.22862963710.662100
1.79-1.844.50.5531.42779761690.553100
1.84-1.94.50.4381.82703759820.438100
1.9-1.964.50.3711.92587657980.371100
1.96-2.034.50.2892.62544156150.289100
2.03-2.114.50.2313.22471654570.231100
2.11-2.194.50.1814.12375152430.181100
2.19-2.294.30.1693.62088148810.16997.2
2.29-2.44.50.1335.42177248070.133100
2.4-2.534.50.1175.82094846200.117100
2.53-2.694.50.1056.31963143280.105100
2.69-2.874.50.0946.91862841180.094100
2.87-3.14.50.0847.41734338260.084100
3.1-3.44.50.0679.31598935500.067100
3.4-3.84.50.05810.71439032180.058100
3.8-4.394.50.05210.61274728510.052100
4.39-5.384.40.04711.91079424470.047100
5.38-7.64.30.04613.9829419380.046100
7.6-29.22340.03915439811030.03998.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→29.223 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 4.785 / SU ML: 0.068 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.099
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. CMK MOLECULES (CMP-2-keto-3-deoxy-octulosonic acid)
RfactorNum. reflection% reflectionSelection details
Rfree0.197 4437 5 %RANDOM
Rwork0.172 ---
obs0.173 88524 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 63.24 Å2 / Biso mean: 18.583 Å2 / Biso min: 5.62 Å2
Baniso -1Baniso -2Baniso -3
1--1.15 Å20 Å20 Å2
2---0.22 Å20 Å2
3---1.37 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.223 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5871 0 180 725 6776
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0226511
X-RAY DIFFRACTIONr_bond_other_d0.0020.024293
X-RAY DIFFRACTIONr_angle_refined_deg1.4462.0118938
X-RAY DIFFRACTIONr_angle_other_deg0.977310747
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0345894
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.34525.508236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.78151184
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0631522
X-RAY DIFFRACTIONr_chiral_restr0.0880.21118
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217098
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021128
X-RAY DIFFRACTIONr_mcbond_it1.11434048
X-RAY DIFFRACTIONr_mcbond_other0.25531652
X-RAY DIFFRACTIONr_mcangle_it2.04456657
X-RAY DIFFRACTIONr_scbond_it3.88982463
X-RAY DIFFRACTIONr_scangle_it6.256112219
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 1081 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
ATIGHT POSITIONAL0.070.15
BTIGHT POSITIONAL0.070.15
CTIGHT POSITIONAL0.080.15
DTIGHT POSITIONAL0.080.15
AMEDIUM POSITIONAL0.230.5
BMEDIUM POSITIONAL0.240.5
CMEDIUM POSITIONAL0.230.5
DMEDIUM POSITIONAL0.240.5
ATIGHT THERMAL0.190.5
BTIGHT THERMAL0.190.5
CTIGHT THERMAL0.190.5
DTIGHT THERMAL0.190.5
AMEDIUM THERMAL0.161
BMEDIUM THERMAL0.181
CMEDIUM THERMAL0.171
DMEDIUM THERMAL0.181
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 344 -
Rwork0.283 6113 -
all-6457 -
obs--99.77 %
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)
10.4818-0.04340.05130.5239-0.26990.4384-0.00080.03310.04340.0216-0.061-0.1069-0.05210.07610.06180.0106-0.01110.00470.01680.00860.047579.048562.579217.0324
20.3430.0690.04290.4266-0.21820.5-0.00620.05590.0176-0.05010.01150.02430.0205-0.0305-0.00530.009-0.00160.00420.0133-0.00020.018161.754658.32438.5698
30.4812-0.0539-0.02430.4303-0.25290.49730.0059-0.0579-0.02740.06550.06070.0607-0.0329-0.0885-0.06650.01490.00280.01620.02710.00930.028456.865545.565734.7758
40.5353-0.0064-0.12370.4945-0.24670.4146-0.0057-0.0336-0.035-0.0052-0.0156-0.03490.04480.04170.02120.00680.00430.00260.00540.00090.023774.040136.92730.6864
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 191
2X-RAY DIFFRACTION1B500
3X-RAY DIFFRACTION2B-4 - 193
4X-RAY DIFFRACTION2A500
5X-RAY DIFFRACTION3C0 - 191
6X-RAY DIFFRACTION3D500
7X-RAY DIFFRACTION4D-4 - 193
8X-RAY DIFFRACTION4C500

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