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- PDB-3fna: Crystal structure of the CBS pair of possible D-arabinose 5-phosp... -

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Basic information

Entry
Database: PDB / ID: 3fna
TitleCrystal structure of the CBS pair of possible D-arabinose 5-phosphate isomerase yrbH from Escherichia coli CFT073
ComponentsPossible arabinose 5-phosphate isomerase
KeywordsISOMERASE / CBS pair / structural genomics / D-arabinose 5-phosphate isomerase / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / CBS domain / Lipopolysaccharide biosynthesis
Function / homologyCBS-domain / CBS-domain / Roll / Alpha Beta / ADENOSINE MONOPHOSPHATE
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsCuff, M.E. / Bigelow, L. / Buck, K. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: The CBS Pair of possible D-arabinose 5-phosphate isomerase yrbH from Escherichia coli CFT073
Authors: Cuff, M.E. / Bigelow, L. / Buck, K. / Joachimiak, A.
History
DepositionDec 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 9, 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_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_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)34,2014
Polymers33,5062
Non-polymers6942
Water1,18966
1
A: Possible arabinose 5-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1002
Polymers16,7531
Non-polymers3471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Possible arabinose 5-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1002
Polymers16,7531
Non-polymers3471
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: Possible arabinose 5-phosphate isomerase
hetero molecules

B: Possible arabinose 5-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2014
Polymers33,5062
Non-polymers6942
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_455x-1/2,-y+1/2,-z1
Buried area2000 Å2
ΔGint-13.9 kcal/mol
Surface area11950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.109, 108.458, 104.849
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

#1: Protein Possible arabinose 5-phosphate isomerase


Mass: 16753.100 Da / Num. of mol.: 2 / Fragment: Residues 187-332
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: CFT073 / Gene: c3957 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION.

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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: 2.13 Å3/Da / Density % sol: 42.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 0.1M CHES pH 9.5, 20% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97937, 0.97923
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Dec 13, 2008
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979371
20.979231
ReflectionRedundancy: 9.6 % / Av σ(I) over netI: 45.14 / Number: 180513 / Rmerge(I) obs: 0.093 / Χ2: 2.69 / D res high: 2.03 Å / D res low: 50 Å / Num. obs: 18777 / % possible obs: 99.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.515091.910.10314.0338.5
4.375.519810.0768.179.2
3.824.3798.510.0695.7439.4
3.473.8299.210.0865.1169.5
3.223.4799.510.0833.5689.6
3.033.2299.710.0942.869.7
2.883.0399.810.1082.3569.8
2.762.8899.810.1251.9579.8
2.652.7699.910.1321.6789.8
2.562.6599.910.1491.389.9
2.482.5699.910.1721.059.8
2.412.4810010.1930.9669.8
2.342.4110010.2020.9449.9
2.292.3410010.2480.9229.8
2.232.2910010.2610.9059.8
2.192.2310010.3210.8429.8
2.142.1910010.3720.739.8
2.12.1410010.4490.769.7
2.072.199.910.5340.6799.4
2.032.0799.810.5870.7039.3
ReflectionResolution: 2.03→50 Å / Num. all: 18777 / Num. obs: 18777 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 9.6 % / Biso Wilson estimate: 45.8 Å2 / Rmerge(I) obs: 0.093 / Χ2: 2.688 / Net I/σ(I): 45.14
Reflection shellResolution: 2.03→2.07 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.587 / Num. unique all: 946 / Χ2: 0.703 / % possible all: 99.8

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Phasing

PhasingMethod: MAD
Phasing MADD res high: 2.03 Å / D res low: 50 Å / FOM : 0.424 / FOM acentric: 0.441 / FOM centric: 0.285 / Reflection: 18727 / Reflection acentric: 16730 / Reflection centric: 1997
Phasing MAD set

Highest resolution: 2.03 Å / Lowest resolution: 50 Å

IDR cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
11.6210.30.300167301997
20.850.7811.416.40.840.77131281660
Phasing MAD set shell
IDResolution (Å)R cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
112.65-501.1711.30.9004532
17.24-12.651.1511.50.90024291
15.07-7.241.9311.40.800665151
13.9-5.071.0410.80.7001242215
13.17-3.91.2910.50.4002022276
12.67-3.172.0710.30.1002984359
12.31-2.673.4810.20004107397
12.03-2.319.8210.10005423476
212.65-500.920.6924.732.61.971.614532
27.24-12.650.70.7422.727.81.971.424186
25.07-7.240.650.6617.522.11.841.27665150
23.9-5.070.770.6617.521.61.210.951241213
23.17-3.90.850.7814.418.70.880.72019269
22.67-3.170.890.881013.50.70.52978353
22.31-2.670.960.988.410.90.420.274097394
22.03-2.310.990.988.711.60.250.181842163
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se39.83596-0.225-0.126-0.0610
2Se42.47618-0.547-0.235-0.1020
3Se41.90104-0.513-0.129-0.0640
4Se57.7012-0.475-0.0920.0190
5Se42.06295-0.626-0.144-0.1530
6Se55.33124-0.585-0.283-0.0820
7Se42.52646-0.686-0.339-0.0480
8Se43.8018-0.651-0.057-0.080
9Se70.44505-0.498-0.033-0.1030
10Se56.92918-0.094-0.067-0.1120
11Se68.30847-0.119-0.161-0.0460
12Se47.27854-0.115-0.0630.0040
13Se58.82204-0.267-0.168-0.140
14Se46.7346-0.578-0.177-0.0450
15Se73.0979-0.65-0.297-0.0750
16Se67.17161-0.252-0.038-0.1170
17Se55.03701-0.623-0.164-0.0430
18Se63.19827-0.298-0.056-0.1460
19Se51.54322-0.449-0.021-0.0720
20Se44.18999-0.225-0.126-0.061-0.172
21Se47.73014-0.548-0.236-0.101-0.146
22Se46.87647-0.514-0.129-0.064-0.123
23Se65.73748-0.474-0.0920.019-0.107
24Se46.4326-0.627-0.143-0.154-0.098
25Se66.8315-0.585-0.283-0.082-0.152
26Se48.33464-0.685-0.339-0.047-0.135
27Se47.53928-0.651-0.059-0.08-0.126
28Se74.57764-0.497-0.033-0.103-0.095
29Se63.95687-0.092-0.067-0.112-0.135
30Se68.37031-0.12-0.161-0.047-0.096
31Se53.05678-0.115-0.0630.004-0.091
32Se61.79441-0.268-0.168-0.14-0.1
33Se66.63028-0.579-0.177-0.045-0.109
34Se71.60002-0.65-0.298-0.074-0.125
35Se66.88232-0.252-0.038-0.119-0.076
36Se70.19363-0.623-0.164-0.043-0.051
37Se89.027-0.298-0.054-0.145-0.065
38Se62.11614-0.451-0.021-0.073-0.037
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
12.65-500.6640.7480.546774532
7.24-12.650.6940.7710.48833324291
5.07-7.240.7760.8180.59816665151
3.9-5.070.7110.7390.54614571242215
3.17-3.90.6510.680.44522982022276
2.67-3.170.5510.580.3133432984359
2.31-2.670.3680.3910.12845044107397
2.03-2.310.1680.180.03458995423476
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 18727
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
6.76-10058.50.775513
5.38-6.7639.40.915513
4.72-5.3835.70.939503
4.28-4.7237.30.937511
3.97-4.2841.20.928512
3.74-3.9739.20.934506
3.54-3.7438.30.94540
3.37-3.5439.90.937571
3.22-3.3743.80.914603
3.09-3.2244.70.922613
2.98-3.09480.917645
2.87-2.9845.50.902663
2.78-2.8748.90.892687
2.69-2.7846.30.907708
2.62-2.6946.80.903737
2.55-2.6257.10.871761
2.48-2.5555.60.861754
2.42-2.4859.60.856788
2.36-2.4262.50.868817
2.31-2.3663.60.876823
2.26-2.3163.70.867825
2.22-2.2665.40.862865
2.17-2.2272.30.844879
2.13-2.17740.839889
2.09-2.1374.60.851903
2.03-2.0978.50.7631598

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM6phasing
REFMACrefinement
PDB_EXTRACT3.006data 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: 2.1→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.252 / WRfactor Rwork: 0.219 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.881 / SU B: 10.769 / SU ML: 0.134 / SU R Cruickshank DPI: 0.236 / SU Rfree: 0.188 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.231 / ESU R Free: 0.186
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.243 863 5.1 %RANDOM
Rwork0.211 ---
all0.213 16930 --
obs0.213 16930 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 77.2 Å2 / Biso mean: 37.11 Å2 / Biso min: 20.28 Å2
Baniso -1Baniso -2Baniso -3
1--2.22 Å20 Å20 Å2
2---0.15 Å20 Å2
3---2.37 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1860 0 36 66 1962
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212017
X-RAY DIFFRACTIONr_bond_other_d0.0010.021351
X-RAY DIFFRACTIONr_angle_refined_deg1.5622.0072736
X-RAY DIFFRACTIONr_angle_other_deg0.8743.0013279
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5975258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.61822.56182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.35515379
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1251522
X-RAY DIFFRACTIONr_chiral_restr0.0760.2333
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022213
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02384
X-RAY DIFFRACTIONr_mcbond_it0.8171.51256
X-RAY DIFFRACTIONr_mcbond_other0.1691.5518
X-RAY DIFFRACTIONr_mcangle_it1.53122038
X-RAY DIFFRACTIONr_scbond_it2.3633761
X-RAY DIFFRACTIONr_scangle_it3.7764.5698
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 59 -
Rwork0.24 1179 -
all-1238 -
obs--99.44 %
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)
11.759-0.29730.05362.8728-0.30913.83370.1702-0.1363-0.1704-0.102-0.0849-0.12760.0464-0.1808-0.08540.0194-0.0127-0.01230.06880.0750.104621.13817.35085.717
23.58971.5160.20156.01580.33752.76140.2262-0.292-0.73560.0835-0.13-0.8126-0.14510.0688-0.09620.026-0.0084-0.030.11370.16110.371942.213216.5934.5023
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 146
2X-RAY DIFFRACTION2B1 - 146

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