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- PDB-3sc6: 2.65 Angstrom resolution crystal structure of dTDP-4-dehydrorhamn... -

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Basic information

Entry
Database: PDB / ID: 3sc6
Title2.65 Angstrom resolution crystal structure of dTDP-4-dehydrorhamnose reductase (rfbD) from Bacillus anthracis str. Ames in complex with NADP
ComponentsdTDP-4-dehydrorhamnose reductase
KeywordsOXIDOREDUCTASE / dTDP-4-dehydrorhamnose reductase / rfbD / structural genomics / infectious diseases / Bacillus anthracis str. Ames / rhamnose biosynthetic pathway / Center for Structural Genomics of Infectious Diseases / CSGID / Rossmann fold / Catalyzes formation of dTDP-4-dehydro-6-deoxy-L-mannose / NADPH and H+ from dTDP-6-deoxy-L-mannose and NADP+
Function / homology
Function and homology information


dTDP-4-dehydrorhamnose reductase / dTDP-4-dehydrorhamnose reductase activity / dTDP-rhamnose biosynthetic process / nucleotide binding / cytosol
Similarity search - Function
dTDP-4-dehydrorhamnose reductase family / RmlD-like substrate binding domain / RmlD substrate 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / dTDP-4-dehydrorhamnose reductase / dTDP-4-dehydrorhamnose reductase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsHalavaty, A.S. / Kuhn, M. / Shuvalova, L. / Minasov, G. / Peterson, S. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: Structure of the Bacillus anthracis dTDP-L-rhamnose-biosynthetic enzyme dTDP-4-dehydrorhamnose reductase (RfbD).
Authors: Law, A. / Stergioulis, A. / Halavaty, A.S. / Minasov, G. / Anderson, W.F. / Kuhn, M.L.
History
DepositionJun 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 23, 2017Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.pdbx_details
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Dec 13, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._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 1.5Sep 13, 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 / 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 / _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

Downloads & links

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Assembly

Deposited unit
A: dTDP-4-dehydrorhamnose reductase
B: dTDP-4-dehydrorhamnose reductase
C: dTDP-4-dehydrorhamnose reductase
D: dTDP-4-dehydrorhamnose reductase
E: dTDP-4-dehydrorhamnose reductase
F: dTDP-4-dehydrorhamnose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,42029
Polymers196,3276
Non-polymers6,09423
Water4,324240
1
A: dTDP-4-dehydrorhamnose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6574
Polymers32,7211
Non-polymers9363
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: dTDP-4-dehydrorhamnose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8496
Polymers32,7211
Non-polymers1,1285
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: dTDP-4-dehydrorhamnose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6574
Polymers32,7211
Non-polymers9363
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: dTDP-4-dehydrorhamnose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6574
Polymers32,7211
Non-polymers9363
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: dTDP-4-dehydrorhamnose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8496
Polymers32,7211
Non-polymers1,1285
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: dTDP-4-dehydrorhamnose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7535
Polymers32,7211
Non-polymers1,0324
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.449, 113.337, 144.949
Angle α, β, γ (deg.)90.00, 91.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
dTDP-4-dehydrorhamnose reductase


Mass: 32721.137 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames / Gene: BAS1138, BA_1231, GBAA_1231, rfbD / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21/Magic
References: UniProt: Q81TN9, UniProt: A0A6L7H7R4*PLUS, dTDP-4-dehydrorhamnose reductase
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 3.32 Å3/Da / Density % sol: 62.99 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein: 7.5 mg/mL in buffer containing 10 mM Tris HCl pH 8.3, 500 mM NaCl, and 5 mM BME, 5 mM MgCl2, 1 mM NADP+, and 10% glycerol.Crystallization conditions: 0.2 M lithium sulfate, 0.1 M ...Details: Protein: 7.5 mg/mL in buffer containing 10 mM Tris HCl pH 8.3, 500 mM NaCl, and 5 mM BME, 5 mM MgCl2, 1 mM NADP+, and 10% glycerol.Crystallization conditions: 0.2 M lithium sulfate, 0.1 M Tris pH 8.5, and 25% w/v PEG 5000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 3, 2011 / Details: Mirror
RadiationMonochromator: Si(111) Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.65→30 Å / Num. all: 75200 / Num. obs: 75200 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 67.1 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 11.49
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.615 / Mean I/σ(I) obs: 2.35 / Num. unique all: 3724 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VL0

1vl0


Resolution: 2.65→29.9 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.922 / SU B: 26.342 / SU ML: 0.252 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.313 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25785 3745 5 %RANDOM
Rwork0.21531 ---
obs0.21747 70861 99.94 %-
all-70861 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 56.691 Å2
Baniso -1Baniso -2Baniso -3
1-4.94 Å2-0 Å20.53 Å2
2---0.35 Å2-0 Å2
3----4.56 Å2
Refinement stepCycle: LAST / Resolution: 2.65→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13571 0 373 240 14184
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02214435
X-RAY DIFFRACTIONr_bond_other_d0.0010.029585
X-RAY DIFFRACTIONr_angle_refined_deg1.3591.97619635
X-RAY DIFFRACTIONr_angle_other_deg0.791323341
X-RAY DIFFRACTIONr_dihedral_angle_1_deg0.6851697
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.93724.448697
X-RAY DIFFRACTIONr_dihedral_angle_3_deg4.01152403
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.5421568
X-RAY DIFFRACTIONr_chiral_restr0.0830.22102
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215832
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022994
X-RAY DIFFRACTIONr_mcbond_it0.6061.58431
X-RAY DIFFRACTIONr_mcbond_other0.1031.53430
X-RAY DIFFRACTIONr_mcangle_it1.172213646
X-RAY DIFFRACTIONr_scbond_it1.82236004
X-RAY DIFFRACTIONr_scangle_it3.0114.55989
LS refinement shellResolution: 2.65→2.718 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 277 -
Rwork0.338 5134 -
obs-5134 99.45 %
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)
11.7931-0.12180.50591.88730.22921.9821-0.0469-0.1661-0.05010.20110.0669-0.23240.2746-0.0467-0.02010.1311-0.0226-0.03540.15090.02270.178544.5678-49.6462101.2317
21.19410.0994-0.51340.7214-0.74294.1366-0.0531-0.2034-0.03660.25070.1290.066-0.1558-0.4758-0.07590.2403-0.0016-0.01310.25960.05750.031230.5036-47.0668114.9856
30.5173-0.00880.13951.41780.55673.1064-0.0022-0.04420.0556-0.15090.0277-0.02420.0241-0.2046-0.02550.0653-0.01360.00360.1972-0.01950.19333.5225-29.052880.5188
41.5-1.6335-0.25363.40320.8610.30340.03920.09380.1831-0.2315-0.0659-0.161-0.0628-0.0040.02670.15850.01780.00610.1636-0.00660.170334.6099-10.230277.1856
51.6705-0.14510.13882.40951.18522.25390.04920.08720.0015-0.09740.145-0.17770.02840.1117-0.19420.0118-0.01170.01480.1692-0.0670.252864.2233-32.692883.9165
62.79061.10990.72830.6596-0.02440.71450.2046-0.0967-0.19970.0446-0.0751-0.13920.12430.0995-0.12950.03490.0443-0.01380.2275-0.11940.379377.0328-29.97397.3556
70.8083-0.4296-0.52212.0480.42493.2951-0.052-0.1436-0.03860.15750.15320.1336-0.0252-0.1312-0.10120.06120.0397-0.01040.2190.01510.15927.88980.7278135.7855
82.32591.8769-0.13812.1177-0.26870.9191-0.034-0.2339-0.286-0.04590.1361-0.18470.1821-0.0842-0.10220.1779-0.0042-0.04630.24740.12120.148828.0449-18.9579137.3248
91.90040.75620.29592.61330.76542.0102-0.0974-0.1088-0.06740.05870.1231-0.19510.03940.0214-0.02570.02720.0481-0.04560.2204-0.12210.180558.49283.8569132.4388
103.1635-2.4068-1.07443.3610.55780.47260.09750.08960.22480.02560.0286-0.471-0.0776-0.0108-0.12620.04090.0207-0.02110.2233-0.17010.315971.47911.8974118.9778
112.3468-0.00540.05991.60540.91862.7529-0.1178-0.00080.1432-0.1360.1559-0.0777-0.31460.1307-0.0380.16350.03150.01730.0653-0.0030.143738.418423.2175115.7892
120.7259-0.16980.32190.8206-0.36692.80290.07760.0101-0.0364-0.07590.0250.0161-0.2552-0.2677-0.10270.15170.05580.03020.1643-0.01250.136927.768417.5995103.8771
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 144
2X-RAY DIFFRACTION2A145 - 282
3X-RAY DIFFRACTION3B-2 - 142
4X-RAY DIFFRACTION4B143 - 281
5X-RAY DIFFRACTION5C1 - 142
6X-RAY DIFFRACTION6C143 - 281
7X-RAY DIFFRACTION7D-1 - 145
8X-RAY DIFFRACTION8D146 - 281
9X-RAY DIFFRACTION9E2 - 142
10X-RAY DIFFRACTION10E143 - 282
11X-RAY DIFFRACTION11F1 - 121
12X-RAY DIFFRACTION12F122 - 281

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