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- PDB-1vl0: CRYSTAL STRUCTURE OF A DTDP-4-DEHYDRORHAMNOSE REDUCTASE, RFBD ORT... -

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Basic information

Entry
Database: PDB / ID: 1vl0
TitleCRYSTAL STRUCTURE OF A DTDP-4-DEHYDRORHAMNOSE REDUCTASE, RFBD ORTHOLOG (CA_C2315) FROM CLOSTRIDIUM ACETOBUTYLICUM ATCC 824 AT 2.05 A RESOLUTION
ComponentsDTDP-4-dehydrorhamnose reductase, rfbD ortholog
KeywordsOXIDOREDUCTASE / DTDP-4-DEHYDRORHAMNOSE REDUCTASE / RFBD ORTHOLOG / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI
Function / homology
Function and homology information


dTDP-4-dehydrorhamnose reductase / dTDP-4-dehydrorhamnose reductase activity / dTDP-rhamnose biosynthetic process / nucleotide binding
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
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Unknown ligand / dTDP-4-dehydrorhamnose reductase
Similarity search - Component
Biological speciesClostridium acetobutylicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of DTDP-4-dehydrorhamnose reductase, rfbD ortholog (CAC2315) from Clostridium acetobutylicum at 2.05 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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, rfbD ortholog
B: DTDP-4-dehydrorhamnose reductase, rfbD ortholog
C: DTDP-4-dehydrorhamnose reductase, rfbD ortholog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,7927
Polymers99,7963
Non-polymers1,9964
Water8,125451
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8340 Å2
ΔGint-48 kcal/mol
Surface area32930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.800, 130.670, 151.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: MSE / End label comp-ID: GLN / Refine code: 1 / Auth seq-ID: 1 - 279 / Label seq-ID: 13 - 291

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC

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Components

#1: Protein DTDP-4-dehydrorhamnose reductase, rfbD ortholog


Mass: 33265.172 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium acetobutylicum (bacteria) / Strain: ATCC 824 / Gene: CAC2315 / Production host: Escherichia coli (E. coli) / References: UniProt: Q97GQ1
#2: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 451 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.6453.4
22.6252.64
Crystal grow
Temperature (K)Crystal-IDMethodDetails
2771vapor diffusion, sitting drop, nanodrop0.06M MES, 0.04M MES_Na, 2% NP_PEG MME 2000 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
2772vapor diffusion, sitting drop, nanodrop0.06M MES, 0.04M MES_Na, 2% NP_PEG MME 2000 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONALS 8.2.111
SYNCHROTRONALS 8.2.120.9795,0.9796
DetectorType: ADSC / Detector: CCD / Date: Mar 10, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double Crystal Si(111)SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97951
30.97961
ReflectionResolution: 2.05→19.99 Å / Num. obs: 66292 / % possible obs: 99.9 % / Redundancy: 4.9 % / Biso Wilson estimate: 40.95 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 12.5
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.572 / Mean I/σ(I) obs: 2.3 / Num. unique all: 9628 / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA(CCP4 4.2)data scaling
SOLVEphasing
RESOLVEmodel building
REFMAC5.2.0003refinement
CCP4(SCALA)data scaling
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.05→19.99 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 9.071 / SU ML: 0.121 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. AN UNKNOWN ENTITY BOUND TO CHAIN A WAS ASSIGNED AS UNKNOWN LIGAND, UNL. 3. OCCUPANCY FOR THE NADH BOUND TO CHAIN A WAS SET TO 0.5.
RfactorNum. reflection% reflectionSelection details
Rfree0.20701 2667 4 %RANDOM
Rwork0.16921 ---
obs0.17072 63619 99.86 %-
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: 38.75 Å2
Baniso -1Baniso -2Baniso -3
1-2.66 Å20 Å20 Å2
2---0.29 Å20 Å2
3----2.37 Å2
Refinement stepCycle: LAST / Resolution: 2.05→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6583 0 149 451 7183
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0226879
X-RAY DIFFRACTIONr_bond_other_d0.0020.026157
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.9719369
X-RAY DIFFRACTIONr_angle_other_deg0.953314372
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8115839
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.44525.522297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.012151163
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1691522
X-RAY DIFFRACTIONr_chiral_restr0.090.21084
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027503
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021261
X-RAY DIFFRACTIONr_nbd_refined0.2040.21272
X-RAY DIFFRACTIONr_nbd_other0.1870.25905
X-RAY DIFFRACTIONr_nbtor_other0.090.23620
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2397
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3220.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2790.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.29
X-RAY DIFFRACTIONr_mcbond_it2.18134519
X-RAY DIFFRACTIONr_mcbond_other0.3231708
X-RAY DIFFRACTIONr_mcangle_it2.77956818
X-RAY DIFFRACTIONr_scbond_it5.13882983
X-RAY DIFFRACTIONr_scangle_it6.85112551
X-RAY DIFFRACTIONr_nbtor_refined0.1810.23399
X-RAY DIFFRACTIONr_symmetry_hbond_other0.110.21
Refine LS restraints NCS

Ens-ID: 1 / Number: 4142 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.040.05
2Btight positional0.040.05
3Ctight positional0.040.05
1Atight thermal0.20.5
2Btight thermal0.20.5
3Ctight thermal0.190.5
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 191 3.92 %
Rwork0.274 4678 -
obs--99.98 %
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)
10.35620.07960.3050.27240.29351.16120.0251-0.0264-0.03160.025-0.03260.01020.1643-0.08960.0075-0.0812-0.07410.01730.01150.02140.001225.61127.79611.596
20.9839-0.2002-0.31720.8316-0.44132.1822-0.0025-0.0255-0.1117-0.0067-0.0366-0.00840.40250.17680.0392-0.1022-0.00180.023-0.04970.0125-0.108438.61124.60931.698
30.42760.2853-0.05210.58680.06660.87460.0212-0.01090.0598-0.0717-0.01250.0106-0.0804-0.076-0.0086-0.0953-0.00690.0167-0.05090.0010.036228.97949.292-10.545
41.27770.46560.09432.62290.34171.76190.02120.08720.2604-0.37430.0901-0.3405-0.29610.1745-0.1113-0.0852-0.10870.1139-0.1088-0.01540.094945.57465.849-16.553
50.5454-0.12550.0580.943-0.23630.8501-0.01830.0123-0.1018-0.1162-0.0021-0.08050.2325-0.03090.0204-0.0064-0.04550.0175-0.0152-0.01680.01327.68119.146-18.226
62.6354-1.4044-0.26712.470.23254.00790.06070.4555-0.2238-0.2326-0.1105-0.25390.46510.56240.04980.16480.07870.12960.1106-0.09150.094542.5763.027-28.086
78.25574.43128.50262.57933.52714.1071-0.10510.1016-0.20850.41580.49650.23870.2893-0.1555-0.39140.0454-0.0529-0.0325-0.08490.00580.091826.5820.47116.305
88.91757.7681-5.229510.7274-7.2554.90680.4393-0.24460.2886-0.3723-0.33550.5652-0.74250.1369-0.10380.0564-0.14690.0032-0.0438-0.04440.035930.74356.794-6.351
90.80312.87841.483610.31625.31732.74070.16260.33160.3046-1.41370.1587-0.69790.4936-0.1702-0.32130.0395-0.01440.13280.0498-0.01750.115130.22818.623-26.723
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 152
2X-RAY DIFFRACTION1A179 - 212
3X-RAY DIFFRACTION1A247 - 267
4X-RAY DIFFRACTION2A153 - 178
5X-RAY DIFFRACTION2A213 - 246
6X-RAY DIFFRACTION2A268 - 280
7X-RAY DIFFRACTION3B1 - 152
8X-RAY DIFFRACTION3B179 - 212
9X-RAY DIFFRACTION3B247 - 267
10X-RAY DIFFRACTION4B153 - 178
11X-RAY DIFFRACTION4B213 - 246
12X-RAY DIFFRACTION4B268 - 280
13X-RAY DIFFRACTION5C0 - 152
14X-RAY DIFFRACTION5C179 - 212
15X-RAY DIFFRACTION5C247 - 267
16X-RAY DIFFRACTION6C153 - 178
17X-RAY DIFFRACTION6C213 - 246
18X-RAY DIFFRACTION6C268 - 280
19X-RAY DIFFRACTION7A300
20X-RAY DIFFRACTION8B300
21X-RAY DIFFRACTION9C300

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