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- PDB-3k2v: Structure of the CBS pair of a putative D-arabinose 5-phosphate i... -

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Basic information

Entry
Database: PDB / ID: 3k2v
TitleStructure of the CBS pair of a putative D-arabinose 5-phosphate isomerase from Klebsiella pneumoniae subsp. pneumoniae.
Componentsputative D-arabinose 5-phosphate isomerase
KeywordsISOMERASE / KpsF-like protein / CBS domain / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


arabinose-5-phosphate isomerase / arabinose-5-phosphate isomerase activity / carbohydrate derivative metabolic process / carbohydrate derivative binding / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Phosphosugar isomerase, KdsD/KpsF-type / : / KpsF-like, SIS domain / SIS domain / CBS-domain / CBS-domain / SIS domain / SIS domain profile. / SIS domain superfamily / CBS domain superfamily ...Phosphosugar isomerase, KdsD/KpsF-type / : / KpsF-like, SIS domain / SIS domain / CBS-domain / CBS-domain / SIS domain / SIS domain profile. / SIS domain superfamily / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-CMK / Arabinose 5-phosphate isomerase
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsCuff, M.E. / Volkart, L. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: Structure of the CBS pair of a putative D-arabinose 5-phosphate isomerase from Klebsiella pneumoniae subsp. pneumoniae.
Authors: Cuff, M.E. / Volkart, L. / Bearden, J. / Joachimiak, A.
History
DepositionSep 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_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

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Assembly

Deposited unit
A: putative D-arabinose 5-phosphate isomerase
B: putative D-arabinose 5-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4918
Polymers33,0322
Non-polymers1,4596
Water5,206289
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-24 kcal/mol
Surface area11460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.151, 102.151, 214.850
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
DetailsLikely the AB dimer in the Asymmetric unit.

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Components

#1: Protein putative D-arabinose 5-phosphate isomerase


Mass: 16515.865 Da / Num. of mol.: 2 / Fragment: targeted domain 186-331
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria)
Strain: MGH 78578 / Gene: KPN78578_35760, KPN_03607, yrbH / Plasmid: pMCSG19 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): modified BL21 / References: UniProt: A6TEL6
#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.: 2 / Source method: obtained synthetically / Formula: C17H26N3O15P
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.27 Å3/Da / Density % sol: 62.33 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris pH8.5, 0.2M Ammonium Sulfate, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931, 0.97945
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 2, 2009
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979311
20.979451
ReflectionRedundancy: 12.2 % / Av σ(I) over netI: 35.55 / Number: 388844 / Rmerge(I) obs: 0.108 / Χ2: 2.11 / D res high: 1.95 Å / D res low: 50 Å / Num. obs: 31947 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.29509910.1029.02611.1
4.25.2910010.0754.68511.4
3.674.210010.084.19711.5
3.333.6710010.0863.45311.8
3.13.3310010.0942.93112.1
2.913.110010.1012.36612.3
2.772.9110010.1122.14712.3
2.652.7710010.1221.65212.3
2.542.6510010.1371.51212.4
2.462.5410010.1621.33412.4
2.382.4610010.1611.16412.4
2.312.3810010.1841.0712.4
2.252.3110010.2021.02612.4
2.22.2510010.2210.91812.4
2.152.210010.2670.88312.4
2.12.1510010.3160.87312.4
2.062.110010.3950.82312.4
2.022.0610010.4730.84912.4
1.982.0210010.5260.88712.4
1.951.9810010.6760.98312.4
ReflectionResolution: 1.95→50 Å / Num. all: 31947 / Num. obs: 31947 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 12.2 % / Biso Wilson estimate: 29.1 Å2 / Rmerge(I) obs: 0.108 / Χ2: 2.105 / Net I/σ(I): 8.7
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 12.4 % / Rmerge(I) obs: 0.676 / Num. unique all: 1582 / Χ2: 0.983 / % possible all: 100

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Phasing

PhasingMethod: MAD
Phasing MADD res high: 1.95 Å / D res low: 50 Å / FOM : 0.45 / FOM acentric: 0.463 / FOM centric: 0.311 / Reflection: 31751 / Reflection acentric: 29151 / Reflection centric: 2600
Phasing MAD set

Highest resolution: 1.95 Å / Lowest resolution: 50 Å

IDR cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
11.6210.60.500291512600
20.90.8227.740.50.790.64219262163
Phasing MAD set shell
IDResolution (Å)R cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
112.25-501.2411.81.4008858
16.98-12.251.1811.81.400471133
14.88-6.981.5511.61001172208
13.75-4.881.0711.21.1002193292
13.05-3.751.2110.80.6003525366
12.57-3.051.9110.60.3005163442
12.22-2.572.6210.40.1007138503
11.95-2.224.110.20.1009401598
212.25-500.90.8443.960.71.761.368857
26.98-12.250.730.7439.958.31.920.92471133
24.88-6.980.760.7336.744.11.571.071172208
23.75-4.880.870.7642.355.30.980.72193292
23.05-3.750.890.8335.6450.760.593524366
22.57-3.050.920.8524.434.40.720.465158442
22.22-2.570.960.9420.929.10.520.367110503
21.95-2.220.98122.129.80.350.252210162
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se37.487750.1440.4430.1450
2Se34.965550.0030.440.0740
3Se40.80559-0.2830.2370.0250
4Se35.52641-0.2970.044-0.0180
5Se54.088560.0730.5070.1270
6Se36.87279-0.2680.1150.0350
7Se65.878830.160.3810.0980
8Se45.81907-0.4310.1790.0110
9Se37.54805-0.2720.142-0.060
10Se35.48036-0.5340.029-0.0090
11Se51.311910.1280.4570.090
12Se79.22138-0.2450.183-0.0210
13Se68.27908-0.2390.17-0.0780
14Se53.67192-0.20.178-0.0820
15Se116.90923-0.5130.065-0.010
16Se34.072150.1440.4430.145-0.101
17Se36.807370.0030.4390.074-0.118
18Se42.07629-0.2820.2370.024-0.125
19Se36.9641-0.2960.044-0.018-0.103
20Se54.212490.0730.5060.127-0.129
21Se59.625-0.2690.1120.032-0.133
22Se59.80720.160.380.098-0.108
23Se45.21872-0.4320.180.012-0.11
24Se46.25294-0.2720.142-0.06-0.099
25Se27.21568-0.5330.03-0.009-0.061
26Se67.946430.1270.4560.091-0.116
27Se112.71975-0.2460.181-0.021-0.117
28Se82.25524-0.240.169-0.078-0.133
29Se75.20015-0.20.179-0.083-0.101
30Se96.68912-0.5160.063-0.011-0.072
31Se48.329-0.3030.2410.0470
32Se41.165-0.2660.1170.0360
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
12.25-500.680.7730.5381468858
6.98-12.250.7550.8160.539604471133
4.88-6.980.750.7870.5413801172208
3.75-4.880.6860.7140.47424852193292
3.05-3.750.6310.6530.42238913525366
2.57-3.050.5730.5910.36356055163442
2.22-2.570.4260.4390.23776417138503
1.95-2.220.2080.2190.03499999401598
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 31751
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
7.96-10046.20.874513
6.29-7.9638.20.928508
5.41-6.2939.70.936570
4.81-5.4138.50.946642
4.38-4.81420.945714
4.05-4.38410.946756
3.78-4.0541.70.938822
3.56-3.7842.80.936872
3.37-3.5642.60.934922
3.21-3.3745.80.931965
3.07-3.21440.9291017
2.95-3.0744.40.9321054
2.84-2.9543.50.9331101
2.75-2.8443.40.9291130
2.66-2.7548.30.9281163
2.58-2.6647.20.9341188
2.5-2.5848.40.9251245
2.44-2.5510.9291268
2.37-2.4454.10.9311309
2.32-2.3751.10.9271330
2.26-2.3254.70.931357
2.21-2.2655.40.9341417
2.17-2.2159.30.9231438
2.12-2.1763.40.9251446
2.08-2.1266.50.9161502
2.04-2.0866.60.9091511
2-2.0472.80.8761520
1.95-274.90.8242471

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM6phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.95→41.58 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.962 / WRfactor Rfree: 0.182 / WRfactor Rwork: 0.157 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.928 / SU B: 4.702 / SU ML: 0.063 / SU R Cruickshank DPI: 0.108 / SU Rfree: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.104
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.182 1604 5.1 %RANDOM
Rwork0.156 ---
obs0.157 31749 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.03 Å2 / Biso mean: 23.761 Å2 / Biso min: 9.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20.24 Å20 Å2
2--0.48 Å20 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 1.95→41.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1969 0 95 289 2353
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222225
X-RAY DIFFRACTIONr_bond_other_d0.0010.021474
X-RAY DIFFRACTIONr_angle_refined_deg1.5322.0273041
X-RAY DIFFRACTIONr_angle_other_deg0.9413.0033566
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6235295
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.16122.82692
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.56515404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4921525
X-RAY DIFFRACTIONr_chiral_restr0.0950.2376
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022450
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02427
X-RAY DIFFRACTIONr_mcbond_it0.7911.51354
X-RAY DIFFRACTIONr_mcbond_other0.1981.5564
X-RAY DIFFRACTIONr_mcangle_it1.55722206
X-RAY DIFFRACTIONr_scbond_it2.6693871
X-RAY DIFFRACTIONr_scangle_it4.1944.5824
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 134 -
Rwork0.22 2177 -
all-2311 -
obs--99.36 %
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)
10.98380.2274-0.64760.30910.35253.7692-0.064-0.1133-0.00240.0394-0.1282-0.01780.1484-0.04180.19220.12310.00890.00040.0670.02280.0311-11.705519.289991.3916
21.78441.6181-0.03811.7271-0.25480.80760.1082-0.06780.3018-0.0026-0.09760.30430.0064-0.0684-0.01060.06040.0247-0.02330.0554-0.030.1729-20.42647.230174.9709
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 146
2X-RAY DIFFRACTION2B2 - 146

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