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- PDB-1nyw: The high resolution structures of RmlC from Streptoccus suis in c... -

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Basic information

Entry
Database: PDB / ID: 1nyw
TitleThe high resolution structures of RmlC from Streptoccus suis in complex with dTDP-D-glucose
ComponentsdTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase
KeywordsISOMERASE / Jelly roll-like structure / Beta sheet
Function / homology
Function and homology information


dTDP-4-dehydrorhamnose 3,5-epimerase / dTDP-4-dehydrorhamnose 3,5-epimerase activity / dTDP-rhamnose biosynthetic process / polysaccharide biosynthetic process / cytosol
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
2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALPHA-D-GLUCOSE / dTDP-4-dehydrorhamnose 3,5-epimerase
Similarity search - Component
Biological speciesStreptococcus suis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsDong, C. / Major, L.L. / Allen, A. / Blankenfeldt, W. / Maskell, D. / Naismith, J.H.
CitationJournal: Structure / Year: 2003
Title: High-Resolution Structures of RmlC from Streptococcus suis in Complex with Substrate Analogs Locate the Active Site of This Class of Enzyme
Authors: Dong, C. / Major, L.L. / Allen, A. / Blankenfeldt, W. / Maskell, D. / Naismith, J.H.
History
DepositionFeb 14, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 23, 2012Group: Atomic model / Refinement description
Revision 1.4Feb 14, 2024Group: 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 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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: dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase
B: dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1054
Polymers44,9772
Non-polymers1,1292
Water9,134507
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5600 Å2
ΔGint-27 kcal/mol
Surface area16160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.586, 47.895, 72.417
Angle α, β, γ (deg.)90.00, 99.02, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B
131A
141B
151A
161B
171A
181B
191A
201B
211A
221B
231A
241B
251A
261B
271A
281B
291A
301B
311A
321B
331A
341B
351A
361B
371A
381B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUPROPRO2AA22 - 2722 - 27
21LEULEUPROPRO2BB22 - 2722 - 27
32LEULEUSERSER2AA60 - 6760 - 67
42LEULEUSERSER2BB60 - 6760 - 67
53VALVALALAALA4AA71 - 7771 - 77
63VALVALALAALA4BB71 - 7771 - 77
74TRPTRPVALVAL2AA80 - 8680 - 86
84TRPTRPVALVAL2BB80 - 8680 - 86
95GLYGLYGLUGLU2AA90 - 10190 - 101
105GLYGLYGLUGLU2BB90 - 10190 - 101
116GLYGLYILEILE2AA106 - 113106 - 113
126GLYGLYILEILE2BB106 - 113106 - 113
137SERSERPROPRO2AA116 - 122116 - 122
147SERSERPROPRO2BB116 - 122116 - 122
158VALVALVALVAL2AA125 - 131125 - 131
168VALVALVALVAL2BB125 - 131125 - 131
179VALVALVALVAL2AA136 - 142136 - 142
189VALVALVALVAL2BB136 - 142136 - 142
1910PHEPHEMETMET4AA6 - 216 - 21
2010PHEPHEMETMET4BB6 - 216 - 21
2111PROPROLYSLYS4AA27 - 5927 - 59
2211PROPROLYSLYS4BB27 - 5927 - 59
2312ARGARGASNASN6AA68 - 7068 - 70
2412ARGARGASNASN6BB68 - 7068 - 70
2513GLUGLUPROPRO6AA78 - 7978 - 79
2613GLUGLUPROPRO6BB78 - 7978 - 79
2714ALAALAGLYGLY6AA87 - 8987 - 89
2814ALAALAGLYGLY6BB87 - 8987 - 89
2915GLYGLYPHEPHE6AA102 - 105102 - 105
3015GLYGLYPHEPHE6BB102 - 105102 - 105
3116ASPASPALAALA6AA114 - 115114 - 115
3216ASPASPALAALA6BB114 - 115114 - 115
3317ARGARGGLYGLY6AA123 - 124123 - 124
3417ARGARGGLYGLY6BB123 - 124123 - 124
3518LEULEUPHEPHE6AA132 - 135132 - 135
3618LEULEUPHEPHE6BB132 - 135132 - 135
3719ASNASNLEULEU5AA143 - 197143 - 197
3819ASNASNLEULEU5BB143 - 197143 - 197

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Components

#1: Protein dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase / E.C.5.1.3.13 / dTDP-4-dehydrorhamnose 3 / 5-epimerase


Mass: 22488.295 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus suis (bacteria) / Strain: serotype 2 / Gene: rmlc / Plasmid: pET21(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q8GIQ0, dTDP-4-dehydrorhamnose 3,5-epimerase
#2: Chemical ChemComp-DAU / 2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALPHA-D-GLUCOSE


Mass: 564.329 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H26N2O16P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 507 / 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: 1.66 Å3/Da / Density % sol: 25.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.4
Details: 0.1 M Tris, 4 mM NiCl2,40% PEG 2000, pH 8.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
17 mg/mlprotein1drop
20.1 MTris-HCl1reservoirpH8.4
34 mM1reservoirNiCl2
440 %PEG20001reservoir
520 mMdTDP-D-glucose1drop

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Details: Diamond
RadiationMonochromator: Diamond(111), Ge(220), Toroidal mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.6→29.88 Å / Num. all: 43875 / Num. obs: 43352 / % possible obs: 95.7 % / Observed criterion σ(F): 1.151 / Observed criterion σ(I): 1.8 / Redundancy: 3.5 % / Biso Wilson estimate: 24.3 Å2 / Rmerge(I) obs: 0.098 / Rsym value: 0.083 / Net I/σ(I): 5.2
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 1.8 / Num. unique all: 5230 / Rsym value: 0.292 / % possible all: 79.8
Reflection
*PLUS
Lowest resolution: 44.28 Å / Num. measured all: 383364 / Rmerge(I) obs: 0.083
Reflection shell
*PLUS
% possible obs: 79.8 % / Rmerge(I) obs: 0.292

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
REFMAC5.1.19refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.6→29.88 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.346 / SU ML: 0.082 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21679 2190 5.1 %RANDOM
Rwork0.17257 ---
all0.175 43352 --
obs0.17486 41144 95.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.893 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å2-0.09 Å2
2---0.88 Å20 Å2
3---0.33 Å2
Refine analyzeLuzzati coordinate error free: 0.108 Å
Refinement stepCycle: LAST / Resolution: 1.6→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3145 0 72 507 3724
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0213318
X-RAY DIFFRACTIONr_bond_other_d0.0030.022868
X-RAY DIFFRACTIONr_angle_refined_deg1.8221.9714513
X-RAY DIFFRACTIONr_angle_other_deg0.97936712
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6255389
X-RAY DIFFRACTIONr_chiral_restr0.1170.2468
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023665
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02695
X-RAY DIFFRACTIONr_nbd_refined0.2020.2667
X-RAY DIFFRACTIONr_nbd_other0.2590.23412
X-RAY DIFFRACTIONr_nbtor_other0.0890.21866
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.2373
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.231
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2440.289
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2290.270
X-RAY DIFFRACTIONr_mcbond_it1.5931.51943
X-RAY DIFFRACTIONr_mcangle_it2.04323125
X-RAY DIFFRACTIONr_scbond_it2.68831375
X-RAY DIFFRACTIONr_scangle_it3.684.51388
X-RAY DIFFRACTIONr_rigid_bond_restr1.62723318
X-RAY DIFFRACTIONr_sphericity_free3.5162507
X-RAY DIFFRACTIONr_sphericity_bonded2.30923223
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
944tight positional0.070.05
1725medium positional0.780.5
282loose positional0.735
944tight thermal0.740.5
1725medium thermal1.172
282loose thermal1.6310
LS refinement shellResolution: 1.6→1.642 Å / Rfactor Rfree error: 0.108 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 114 -
Rwork0.312 2372 -
obs-2372 79.8 %
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)
10.67120.3541-0.25461.02180.09061.04670.04430.0408-0.10930.01990.03270.00420.0893-0.0506-0.07710.074-0.0064-0.02510.0034-0.00950.0567-2.159-10.7120.417
21.34680.30840.00050.70630.02310.462-0.03550.13620.0164-0.06990.0637-0.0728-0.11860.1328-0.02820.1296-0.04190.01810.058-0.01310.015714.46310.24614.059
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 1974 - 197
2X-RAY DIFFRACTION2BB3 - 1973 - 197
Refinement
*PLUS
Rfactor Rfree: 0.217 / Rfactor Rwork: 0.173
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.019
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.82
LS refinement shell
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 1.64 Å

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