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- PDB-2ixl: RmlC S. suis with dTDP-rhamnose -

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Basic information

Entry
Database: PDB / ID: 2ixl
TitleRmlC S. suis with dTDP-rhamnose
ComponentsDTDP-4-DEHYDRORHAMNOSE 3,5-EPIMERASE
KeywordsISOMERASE / EPIMERISE / EPIMERASE / EPIMERIZE
Function / homology
Function and homology information


dTDP-4-dehydrorhamnose 3,5-epimerase / dTDP-4-dehydrorhamnose 3,5-epimerase activity
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
NICKEL (II) ION / 2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE / dTDP-4-dehydrorhamnose 3,5-epimerase
Similarity search - Component
Biological speciesSTREPTOCOCCUS SUIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsDong, C. / Naismith, J.H.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Rmlc, a C3' and C5' Carbohydrate Epimerase, Appears to Operate Via an Intermediate with an Unusual Twist Boat Conformation.
Authors: Dong, C. / Major, L.L. / Srikannathasan, V. / Errey, J.C. / Giraud, M.F. / Lam, J.S. / Graninger, M. / Messner, P. / Mcneil, M.R. / Field, R.A. / Whitfield, C. / Naismith, J.H.
History
DepositionJul 8, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 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 / 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_label_seq_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

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,26410
Polymers89,9534
Non-polymers2,3116
Water26,5721475
1
A: DTDP-4-DEHYDRORHAMNOSE 3,5-EPIMERASE
B: DTDP-4-DEHYDRORHAMNOSE 3,5-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1325
Polymers44,9772
Non-polymers1,1553
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: DTDP-4-DEHYDRORHAMNOSE 3,5-EPIMERASE
D: DTDP-4-DEHYDRORHAMNOSE 3,5-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1325
Polymers44,9772
Non-polymers1,1553
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)51.408, 141.526, 53.586
Angle α, β, γ (deg.)90.00, 92.57, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 4 / Auth seq-ID: 5 - 190 / Label seq-ID: 5 - 190

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
DTDP-4-DEHYDRORHAMNOSE 3,5-EPIMERASE / RMLC


Mass: 22488.295 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS SUIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q8GIQ0, dTDP-4-dehydrorhamnose 3,5-epimerase
#2: Chemical
ChemComp-TRH / 2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE


Mass: 548.330 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H26N2O15P2
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1475 / 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: 2.16 Å3/Da / Density % sol: 43.18 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.6→43 Å / Num. obs: 99569 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 6.6
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 4 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 2.8 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→42.68 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.498 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.212 4973 5 %RANDOM
Rwork0.167 ---
obs0.169 94560 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.11 Å2
2---0.06 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.6→42.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6337 0 142 1475 7954
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226665
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.31.9749064
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2485780
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.57524.762336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.608151066
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5631528
X-RAY DIFFRACTIONr_chiral_restr0.0980.2951
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025144
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.22705
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.24360
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2928
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0060.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.281
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1270.2131
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.7260.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8561.54051
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.22226279
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8233092
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5244.52785
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.2437143
X-RAY DIFFRACTIONr_sphericity_free2.91931477
X-RAY DIFFRACTIONr_sphericity_bonded1.51136477
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Number: 1500 / Refine-ID: X-RAY DIFFRACTION

Ens-IDTypeRms dev position (Å)Weight position
1medium positional0.330.5
2medium positional0.670.5
3medium positional0.410.5
1medium thermal0.672
2medium thermal0.692
3medium thermal0.712
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 311 -
Rwork0.178 6386 -
obs--90.41 %

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