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- PDB-6c46: Crystal structure of dTDP-4-dehydrorhamnose 3,5-epimerase from El... -

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Basic information

Entry
Database: PDB / ID: 6c46
TitleCrystal structure of dTDP-4-dehydrorhamnose 3,5-epimerase from Elizabethkingia anophelis NUHP1
ComponentsdTDP-4-dehydrorhamnose 3,5-epimerase
KeywordsISOMERASE / SSGCID / Structural Genomics / Elizabethkingia anophelis / dTDP-4-dehydrorhamnose 3 / 5-epimerase / BD94_3275 / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


dTDP-4-dehydrorhamnose 3,5-epimerase / dTDP-4-dehydrorhamnose 3,5-epimerase activity / dTDP-rhamnose biosynthetic process
Similarity search - Function
dTDP-4-dehydrorhamnose 3,5-epimerase-related / dTDP-4-dehydrorhamnose 3,5-epimerase / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
dTDP-4-dehydrorhamnose 3,5-epimerase
Similarity search - Component
Biological speciesElizabethkingia anophelis NUHP1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of dTDP-4-dehydrorhamnose 3,5-epimerase from Elizabethkingia anophelis NUHP1
Authors: Abendroth, J. / Delker, S.L. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionJan 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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_asym_id / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: dTDP-4-dehydrorhamnose 3,5-epimerase
B: dTDP-4-dehydrorhamnose 3,5-epimerase
C: dTDP-4-dehydrorhamnose 3,5-epimerase
D: dTDP-4-dehydrorhamnose 3,5-epimerase
E: dTDP-4-dehydrorhamnose 3,5-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,5247
Polymers109,4435
Non-polymers802
Water15,961886
1
A: dTDP-4-dehydrorhamnose 3,5-epimerase
B: dTDP-4-dehydrorhamnose 3,5-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8173
Polymers43,7772
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-17 kcal/mol
Surface area16570 Å2
MethodPISA
2
C: dTDP-4-dehydrorhamnose 3,5-epimerase
D: dTDP-4-dehydrorhamnose 3,5-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8173
Polymers43,7772
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-17 kcal/mol
Surface area16830 Å2
MethodPISA
3
E: dTDP-4-dehydrorhamnose 3,5-epimerase

E: dTDP-4-dehydrorhamnose 3,5-epimerase


Theoretical massNumber of molelcules
Total (without water)43,7772
Polymers43,7772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area2360 Å2
ΔGint-8 kcal/mol
Surface area16420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.340, 62.240, 131.020
Angle α, β, γ (deg.)90.000, 105.020, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-391-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid -1 through 14 or resid 16...
21(chain B and (resid -1 through 14 or resid 16...
31(chain C and (resid -1 through 14 or resid 16...
41(chain D and ((resid -1 and (name N or name...
51(chain E and (resid -1 through 14 or resid 16...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISILEILE(chain A and (resid -1 through 14 or resid 16...AA-1 - 147 - 22
12PROPROPROPRO(chain A and (resid -1 through 14 or resid 16...AA1624
13VALVALGLUGLU(chain A and (resid -1 through 14 or resid 16...AA18 - 2026 - 28
14ASPASPASPASP(chain A and (resid -1 through 14 or resid 16...AA2129
15HISHISCACA(chain A and (resid -1 through 14 or resid 16...AA - F-1 - 2007
16HISHISCACA(chain A and (resid -1 through 14 or resid 16...AA - F-1 - 2007
17HISHISCACA(chain A and (resid -1 through 14 or resid 16...AA - F-1 - 2007
18HISHISCACA(chain A and (resid -1 through 14 or resid 16...AA - F-1 - 2007
21HISHISILEILE(chain B and (resid -1 through 14 or resid 16...BB-1 - 147 - 22
22PROPROPROPRO(chain B and (resid -1 through 14 or resid 16...BB1624
23VALVALPHEPHE(chain B and (resid -1 through 14 or resid 16...BB18 - 1926 - 27
24GLUGLUASPASP(chain B and (resid -1 through 14 or resid 16...BB20 - 2128 - 29
25HISHISTYRTYR(chain B and (resid -1 through 14 or resid 16...BB-1 - 1817 - 189
26HISHISTYRTYR(chain B and (resid -1 through 14 or resid 16...BB-1 - 1817 - 189
27HISHISTYRTYR(chain B and (resid -1 through 14 or resid 16...BB-1 - 1817 - 189
28HISHISTYRTYR(chain B and (resid -1 through 14 or resid 16...BB-1 - 1817 - 189
31HISHISILEILE(chain C and (resid -1 through 14 or resid 16...CC-1 - 147 - 22
32PROPROPROPRO(chain C and (resid -1 through 14 or resid 16...CC1624
33VALVALPHEPHE(chain C and (resid -1 through 14 or resid 16...CC18 - 1926 - 27
34GLUGLUARGARG(chain C and (resid -1 through 14 or resid 16...CC20 - 2328 - 31
35HISHISTYRTYR(chain C and (resid -1 through 14 or resid 16...CC-1 - 1817 - 189
36HISHISTYRTYR(chain C and (resid -1 through 14 or resid 16...CC-1 - 1817 - 189
37HISHISTYRTYR(chain C and (resid -1 through 14 or resid 16...CC-1 - 1817 - 189
38HISHISTYRTYR(chain C and (resid -1 through 14 or resid 16...CC-1 - 1817 - 189
41HISHISHISHIS(chain D and ((resid -1 and (name N or name...DD-17
42HISHISCACA(chain D and ((resid -1 and (name N or name...DD - G-1 - 2007
43HISHISCACA(chain D and ((resid -1 and (name N or name...DD - G-1 - 2007
44HISHISCACA(chain D and ((resid -1 and (name N or name...DD - G-1 - 2007
45HISHISCACA(chain D and ((resid -1 and (name N or name...DD - G-1 - 2007
51HISHISILEILE(chain E and (resid -1 through 14 or resid 16...EE-1 - 147 - 22
52PROPROPROPRO(chain E and (resid -1 through 14 or resid 16...EE1624
53VALVALPHEPHE(chain E and (resid -1 through 14 or resid 16...EE18 - 1926 - 27
54GLUGLUASPASP(chain E and (resid -1 through 14 or resid 16...EE20 - 2128 - 29
55HISHISTYRTYR(chain E and (resid -1 through 14 or resid 16...EE-1 - 1817 - 189
56HISHISTYRTYR(chain E and (resid -1 through 14 or resid 16...EE-1 - 1817 - 189
57HISHISTYRTYR(chain E and (resid -1 through 14 or resid 16...EE-1 - 1817 - 189
58HISHISTYRTYR(chain E and (resid -1 through 14 or resid 16...EE-1 - 1817 - 189

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Components

#1: Protein
dTDP-4-dehydrorhamnose 3,5-epimerase / Thymidine diphospho-4-keto-rhamnose 3 / 5-epimerase


Mass: 21888.670 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Elizabethkingia anophelis NUHP1 (bacteria)
Gene: BD94_3275 / Plasmid: ElanA.18372.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A077ENB9, dTDP-4-dehydrorhamnose 3,5-epimerase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 886 / Source method: isolated from a natural source / Formula: H2O

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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: 2.51 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 22.4 mg/mL ElanA.18372.a.B1 with Molecular Dimensions Morpheus screen A2 (10% w/v PEG20000, 20% v/v PEG550 MME, 30 mM magnesium chloride, 30 mM calcium chloride, 100 mM MES/imidazole, pH 6.5) ...Details: 22.4 mg/mL ElanA.18372.a.B1 with Molecular Dimensions Morpheus screen A2 (10% w/v PEG20000, 20% v/v PEG550 MME, 30 mM magnesium chloride, 30 mM calcium chloride, 100 mM MES/imidazole, pH 6.5), cryoprotection: direct, tray 296494 A2, puck esb5-10.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Dec 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→40.032 Å / Num. obs: 77001 / % possible obs: 97 % / Redundancy: 12.893 % / Biso Wilson estimate: 23.23 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.08 / Χ2: 1.038 / Net I/σ(I): 23.01
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.95-27.930.5363.8752480.9030.57389.8
2-2.069.080.4285.3152670.940.45492.5
2.06-2.129.7950.3357.1352480.9570.35395.1
2.12-2.1810.7380.288.9752140.9760.29496.7
2.18-2.2511.3690.24810.3250290.9820.2696.9
2.25-2.3312.1490.22711.6749120.9880.23797.4
2.33-2.4213.5390.20913.2647350.9920.21797.6
2.42-2.5215.0530.18915.2946120.9950.19697.9
2.52-2.6315.0570.15617.8844220.9960.16298.1
2.63-2.7615.0620.13420.0241880.9970.13998.4
2.76-2.9115.0340.11223.4340710.9980.11698.5
2.91-3.0815.0470.08929.138300.9990.09298.9
3.08-3.314.9530.06837.9336300.9990.07199
3.3-3.5614.8040.0643.8833570.9990.06299.2
3.56-3.914.5640.04853.6331270.9990.04999.3
3.9-4.3614.5910.04357.83283410.04499.5
4.36-5.0314.5670.03860.24253010.03999.7
5.03-6.1714.9110.04750.6421250.9990.04899.8
6.17-8.7214.6940.04253.4516760.9990.04499.6
8.72-40.03213.7540.03264.3394610.03398.6

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
MoRDaphasing
Cootmodel building
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1DZR

1dzr


Resolution: 1.95→40.032 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.17
RfactorNum. reflection% reflectionSelection details
Rfree0.203 1937 2.52 %0
Rwork0.1603 ---
obs0.1613 76974 97.05 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.22 Å2 / Biso mean: 30.9219 Å2 / Biso min: 4.24 Å2
Refinement stepCycle: final / Resolution: 1.95→40.032 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7250 0 2 900 8152
Biso mean--19.69 38.5 -
Num. residues----914
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3801X-RAY DIFFRACTION6.565TORSIONAL
12B3801X-RAY DIFFRACTION6.565TORSIONAL
13C3801X-RAY DIFFRACTION6.565TORSIONAL
14D3801X-RAY DIFFRACTION6.565TORSIONAL
15E3801X-RAY DIFFRACTION6.565TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-1.99880.22891420.20064907504990
1.9988-2.05280.25691330.18495085521892
2.0528-2.11320.20951330.17565194532795
2.1132-2.18140.18981390.16665322546197
2.1814-2.25940.24451400.16865311545197
2.2594-2.34990.2231230.16715358548197
2.3499-2.45680.22321500.17025390554098
2.4568-2.58630.21911470.17115389553698
2.5863-2.74830.21131280.17225421554998
2.7483-2.96040.19691520.16845444559699
2.9604-3.25820.21241420.16525454559699
3.2582-3.72940.19541180.14785521563999
3.7294-4.69750.1711440.131655645708100
4.6975-40.04030.19291460.163456775823100
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)
12.3067-0.02280.0331.5973-0.04772.1998-0.0565-0.29960.19970.27490.0644-0.0529-0.22170.0098-0.01060.19050.03820.00660.2184-0.01830.132214.6581.012647.6053
23.1466-0.6256-0.31391.9883-0.04872.24290.15110.4289-0.436-0.229-0.09110.22820.0892-0.0119-0.06470.1660.0379-0.00920.3269-0.05690.254-16.6217-9.383749.2469
31.6224-0.01380.03271.0673-0.36351.4128-0.0608-0.03740.1814-0.02210.0507-0.0048-0.1528-0.0420.01010.12750.00860.01450.108-0.00310.133140.5164-0.659211.4382
41.954-0.00410.05251.5488-0.12431.82580.0574-0.1297-0.02850.1286-0.0823-0.12540.02010.05590.030.1237-0.01280.01780.11250.01430.135465.2017-14.257315.6067
52.4351-0.12520.48191.69420.00942.31710.1229-0.0999-0.30360.08340.0720.03130.29010.0102-0.13630.14930.0043-0.01670.13740.02070.165722.9147-20.635631.0398
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'D' and resid -1 through 181)D-1 - 181
2X-RAY DIFFRACTION2(chain 'E' and resid -1 through 181)E-1 - 181
3X-RAY DIFFRACTION3(chain 'A' and resid -1 through 181)A-1 - 181
4X-RAY DIFFRACTION4(chain 'B' and resid -1 through 181)B-1 - 181
5X-RAY DIFFRACTION5(chain 'C' and resid -1 through 181)C-1 - 181

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