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- PDB-6bi4: 2.9 Angstrom Resolution Crystal Structure of dTDP-Glucose 4,6-deh... -

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Basic information

Entry
Database: PDB / ID: 6bi4
Title2.9 Angstrom Resolution Crystal Structure of dTDP-Glucose 4,6-dehydratase (rfbB) from Bacillus anthracis str. Ames in Complex with NAD.
ComponentsdTDP-glucose 4,6-dehydratase
KeywordsLYASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / dTDP-Glucose 4 / 6-dehydratase / NAD
Function / homology
Function and homology information


dTDP-glucose 4,6-dehydratase / dTDP-glucose 4,6-dehydratase activity / nucleotide-sugar metabolic process / nucleotide binding
Similarity search - Function
dTDP-glucose 4,6-dehydratase / GDP-mannose 4,6 dehydratase / NAD(P)-binding domain / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
sucrose / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NICKEL (II) ION / dTDP-glucose 4,6-dehydratase / dTDP-glucose 4,6-dehydratase
Similarity search - Component
Biological speciesBacillus anthracis str. Ames (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsHalavaty, A.S. / Kuhn, M. / Shuvalova, L. / Minasov, G. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: J.Struct.Biol. / Year: 2018
Title: Structure of the Bacillus anthracis dTDP-l-rhamnose biosynthetic pathway enzyme: dTDP-alpha-d-glucose 4,6-dehydratase, RfbB.
Authors: Gokey, T. / Halavaty, A.S. / Minasov, G. / Anderson, W.F. / Kuhn, M.L.
History
DepositionOct 31, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionNov 8, 2017ID: 4EGB
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 27, 2021Group: Database references / Structure summary / Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
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.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
Revision 2.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 2.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: dTDP-glucose 4,6-dehydratase
B: dTDP-glucose 4,6-dehydratase
C: dTDP-glucose 4,6-dehydratase
D: dTDP-glucose 4,6-dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,51726
Polymers159,7164
Non-polymers4,80122
Water1,36976
1
A: dTDP-glucose 4,6-dehydratase
D: dTDP-glucose 4,6-dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,25813
Polymers79,8582
Non-polymers2,40011
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5870 Å2
ΔGint-132 kcal/mol
Surface area24840 Å2
MethodPISA
2
B: dTDP-glucose 4,6-dehydratase
C: dTDP-glucose 4,6-dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,25813
Polymers79,8582
Non-polymers2,40011
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-134 kcal/mol
Surface area24600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.557, 165.557, 292.121
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 0 - 321 / Label seq-ID: 24 - 345

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein / Sugars , 2 types, 6 molecules ABCD

#1: Protein
dTDP-glucose 4,6-dehydratase


Mass: 39928.996 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis str. Ames (bacteria)
Strain: Ames / Gene: rfbB / Plasmid: pMCSG19c / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)Magic
References: UniProt: Q81TP0, UniProt: A0A6L7HMN5*PLUS, dTDP-glucose 4,6-dehydratase
#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 96 molecules

#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.14 Å3/Da / Density % sol: 60.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PROTEIN: TOTAL RFBB AND RFBC AT 7.5 MG/ML IN 10 MM TRIS HCL PH 8.3, 500 MM NACL, 5 MM BME, 10% GLYCEROL, 5 MM MGCL2, AND 1 MM NAD+. SCREEN: 0.1 M TRIS HCL PH 8.0, 1.56 M AMMONIUM SULFATE, ...Details: PROTEIN: TOTAL RFBB AND RFBC AT 7.5 MG/ML IN 10 MM TRIS HCL PH 8.3, 500 MM NACL, 5 MM BME, 10% GLYCEROL, 5 MM MGCL2, AND 1 MM NAD+. SCREEN: 0.1 M TRIS HCL PH 8.0, 1.56 M AMMONIUM SULFATE, AND 8.5% (W/V) PEG3350. CRYO-PROTECTANT SOLUTION: 1:1 RATIO OF 3.6 M AMMONIUM SULFATE AND 50% SUCROSE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 20, 2012 / Details: C(111)
RadiationMonochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 44858 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9.4 % / Biso Wilson estimate: 69.2 Å2 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.051 / Rrim(I) all: 0.158 / Rsym value: 0.15 / Χ2: 1.004 / Net I/σ(I): 13
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.771 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 2208 / CC1/2: 0.843 / Rpim(I) all: 0.256 / Rrim(I) all: 0.813 / Rsym value: 0.771 / Χ2: 1.002 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R66

1r66


Resolution: 2.91→29.95 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / SU B: 25.627 / SU ML: 0.229 / Cross valid method: THROUGHOUT / ESU R: 1.626 / ESU R Free: 0.299 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20436 2264 5 %RANDOM
Rwork0.16742 ---
obs0.16928 42594 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 66.28 Å2
Baniso -1Baniso -2Baniso -3
1--3.8 Å2-0 Å2-0 Å2
2---3.8 Å2-0 Å2
3---7.6 Å2
Refinement stepCycle: 1 / Resolution: 2.91→29.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10012 0 294 76 10382
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01910572
X-RAY DIFFRACTIONr_bond_other_d0.0050.029794
X-RAY DIFFRACTIONr_angle_refined_deg1.6671.99114403
X-RAY DIFFRACTIONr_angle_other_deg1.007322592
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.86451236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.62425.275491
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.72151700
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.031528
X-RAY DIFFRACTIONr_chiral_restr0.1160.21601
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02111700
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022384
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A197970.05
12B197970.05
21A198530.05
22C198530.05
31A196970.06
32D196970.06
41B198700.05
42C198700.05
51B198870.06
52D198870.06
61C199500.05
62D199500.05
LS refinement shellResolution: 2.906→2.981 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 160 -
Rwork0.269 3072 -
obs--99.66 %
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)
13.50410.6334-0.76512.6563-0.34263.3608-0.0043-0.3145-0.16690.0280.1226-0.22970.27650.3155-0.11830.26970.01830.03580.2979-0.11390.0861240.0694-47.236126.3987
21.3061-0.4199-0.41821.92890.47242.13690.0547-0.04720.3561-0.30930.1024-0.2142-0.211-0.0439-0.15710.2392-0.07660.12190.2141-0.10380.1634236.1245-34.00114.7865
32.7070.47760.39392.1960.15522.39340.10860.3280.3628-0.42750.014-0.08620.08-0.0984-0.12250.4527-0.02490.16670.3055-0.03430.1404235.692-40.24734.2997
44.54950.2048-0.02413.61380.37763.00150.0170.29550.0928-0.31320.08550.383-0.2213-0.1053-0.10260.18580.0396-0.04870.2193-0.01940.0583196.6335-37.794941.3614
51.6144-0.8050.46833.16260.31091.60710.1228-0.0639-0.24130.09320.02450.12970.07250.0116-0.14740.13650.0122-0.0460.2717-0.05390.0596203.9718-50.648453.1221
61.38670.08250.4451.96940.43422.09050.1420.248-0.4719-0.23710.01260.12740.19910.0959-0.15460.13760.0068-0.08080.2699-0.14130.1907189.7753-59.530537.7426
74.4277-1.6592-0.19284.0207-0.31033.35510.11820.023-0.0218-0.0562-0.1205-0.38980.05150.43360.00240.11570.0501-0.01880.3133-0.08230.0789236.6884-55.486751.1661
82.1079-0.6178-01.7560.10412.59420.04-0.1673-0.25960.1210.05540.12390.11050.1184-0.09540.16260.0151-0.00920.2269-0.06580.0696223.7299-57.865164.1647
93.6984-0.0569-0.03782.47410.99393.51850.0285-0.2498-0.04830.53140.1622-0.14020.21440.4533-0.19070.170.0778-0.03080.2850.00780.0198230.138-58.43872.0112
103.83660.1971.8494.6203-0.49032.971-0.0327-0.18040.19590.04450.20460.2784-0.113-0.3326-0.17190.15160.02790.08680.289-0.0450.1175211.3329-15.804540.4783
113.6224-0.6081.21592.38011.26671.46070.0597-0.040.1618-0.35150.1457-0.3956-0.09540.0534-0.20540.2957-0.02780.10380.2634-0.12820.1591224.7952-18.376427.173
121.58420.30160.40562.45380.54812.3682-0.0176-0.23110.28670.03810.1311-0.4811-0.13430.1399-0.11350.19810.01590.07330.1686-0.14930.2562229.1021-2.531940.5177
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 97
2X-RAY DIFFRACTION2A98 - 263
3X-RAY DIFFRACTION3A264 - 321
4X-RAY DIFFRACTION4B0 - 97
5X-RAY DIFFRACTION5B98 - 175
6X-RAY DIFFRACTION6B176 - 321
7X-RAY DIFFRACTION7C0 - 97
8X-RAY DIFFRACTION8C98 - 268
9X-RAY DIFFRACTION9C269 - 321
10X-RAY DIFFRACTION10D0 - 97
11X-RAY DIFFRACTION11D98 - 168
12X-RAY DIFFRACTION12D169 - 321

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