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- PDB-8ctr: Crystal Structure of dTDP-4-dehydrorhamnose reductase from Klebsi... -

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Basic information

Entry
Database: PDB / ID: 8ctr
TitleCrystal Structure of dTDP-4-dehydrorhamnose reductase from Klebsiella pneumoniae with bound NADP
ComponentsdTDP-4-dehydrorhamnose reductase
KeywordsOXIDOREDUCTASE / SSGCID / reductase / NADP / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


dTDP-4-dehydrorhamnose reductase / dTDP-4-dehydrorhamnose reductase activity / O antigen biosynthetic process / dTDP-rhamnose biosynthetic process
Similarity search - Function
dTDP-4-dehydrorhamnose reductase family / RmlD-like substrate binding domain / RmlD substrate binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
ACETATE ION / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / dTDP-4-dehydrorhamnose reductase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: to be published
Title: Crystal Structure of dTDP-4-dehydrorhamnose reductase from Klebsiella pneumoniae with bound NADP
Authors: Bolejack, M.J. / Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionMay 16, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,59220
Polymers132,9224
Non-polymers3,67016
Water25,8521435
1
A: dTDP-4-dehydrorhamnose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1485
Polymers33,2301
Non-polymers9184
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: dTDP-4-dehydrorhamnose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1716
Polymers33,2301
Non-polymers9415
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: dTDP-4-dehydrorhamnose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1254
Polymers33,2301
Non-polymers8953
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: dTDP-4-dehydrorhamnose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1485
Polymers33,2301
Non-polymers9184
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.550, 71.690, 81.230
Angle α, β, γ (deg.)89.960, 66.580, 83.080
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
dTDP-4-dehydrorhamnose reductase


Mass: 33230.379 Da / Num. of mol.: 4 / Fragment: KlpnC.17669.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: rmlD, rfbD, rfbD_1, rfbD_2, A7B01_07910, C3F39_24350, DM23092/04_00022, GNE24_11460, SAMEA3649733_05275, SAMEA3727643_01606, SAMEA4873632_01990
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: C9K1F1, dTDP-4-dehydrorhamnose reductase

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Non-polymers , 5 types, 1451 molecules

#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1435 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.85 Å3/Da / Density % sol: 56.87 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein at 22.33 mg/mL was combined with 5 mM NADP and mixed 1:1 (0.2 uL protein and 0.2 uL precipitant) with 0.16M calcium acetate, 0.08M socium cacodylate pH 6.5, 14.4% w/v PEG8000, 20% ...Details: Protein at 22.33 mg/mL was combined with 5 mM NADP and mixed 1:1 (0.2 uL protein and 0.2 uL precipitant) with 0.16M calcium acetate, 0.08M socium cacodylate pH 6.5, 14.4% w/v PEG8000, 20% v/v glycerol (JCSG E11). Cryo: Direct. Puck: ede6-7.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 31, 2022 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.65→45.35 Å / Num. obs: 170335 / % possible obs: 96.2 % / Redundancy: 2.932 % / Biso Wilson estimate: 19.84 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.065 / Χ2: 0.94 / Net I/σ(I): 12.87 / Num. measured all: 499357 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.65-1.692.9910.6612.033733513175124840.6610.80394.8
1.69-1.742.9840.5522.423579112656119930.7270.6794.8
1.74-1.792.9820.4123.153542112504118790.8320.595
1.79-1.842.9940.3174.13426612017114450.8930.38595.2
1.84-1.912.9820.2295.53330211674111660.9420.27895.6
1.91-1.972.9860.1736.933230211298108190.9650.20995.8
1.97-2.052.970.1338.83108910928104680.9770.16295.8
2.05-2.132.9710.10311.032979910416100310.9850.12596.3
2.13-2.222.9510.08512.84287151011097320.9890.10396.3
2.22-2.332.9390.06715.3327208958692590.9930.08296.6
2.33-2.462.9260.05917.0426056919389050.9940.07396.9
2.46-2.612.910.05418.6124356861783710.9950.06697.1
2.61-2.792.880.0462122823814779260.9960.05697.3
2.79-3.012.8450.04123.1921017757573880.9960.0597.5
3.01-3.32.8120.03525.4319095694367910.9970.04397.8
3.3-3.692.8020.03227.6917298629161730.9970.03998.1
3.69-4.262.8230.0329.2915385555454490.9980.03698.1
4.26-5.222.8190.02829.9812927468545860.9980.03497.9
5.22-7.382.7880.0329.079891362935480.9980.03797.8
7.38-45.352.7480.02730.095281199519220.9980.03396.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1n2s

1n2s


Resolution: 1.65→45.35 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 18.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1843 2059 1.21 %
Rwork0.1616 168254 -
obs0.1619 170313 96.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.03 Å2 / Biso mean: 26.7604 Å2 / Biso min: 10.04 Å2
Refinement stepCycle: final / Resolution: 1.65→45.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9050 0 428 1436 10914
Biso mean--33.34 36.64 -
Num. residues----1191
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.690.30851450.2658110371118295
1.69-1.730.2621410.2417110541119595
1.73-1.780.23571330.2194110661119995
1.78-1.830.22641560.1981110721122895
1.83-1.890.20381370.1865111121124995
1.89-1.960.20861340.1872111231125796
1.96-2.030.24211240.1797112101133496
2.03-2.130.20061450.1661111771132296
2.13-2.240.18321180.1626112721139096
2.24-2.380.16691400.1597112811142197
2.38-2.560.18051490.1574112891143897
2.56-2.820.18871410.1579113031144498
2.82-3.230.16521450.153114051155098
3.23-4.070.15531340.1353114181155298
4.07-45.350.16541170.1487114351155298
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)
11.17340.7941-0.48124.3464-1.25192.39040.0470.078-0.2024-0.31710.10410.20450.4973-0.1539-0.11720.2367-0.0354-0.04010.13020.00980.1601-6.77388.3474-32.7377
22.3053-2.03940.48734.3189-0.79050.84910.1308-0.1726-0.2865-0.02140.10920.7960.1044-0.334-0.21390.2076-0.04170.00820.25930.07330.2755-20.368517.4749-23.3559
32.1891-0.97830.93672.103-0.98742.13830.01460.01320.1266-00.0340.1439-0.0323-0.1561-0.03650.1004-0.01710.02090.080.01330.1283-13.04726.7693-32.9196
41.3594-0.21210.37370.975-0.28651.71690.03350.0310.1749-0.00930.01650.1894-0.1133-0.1955-0.03840.13290.01070.01140.09840.01410.1849-15.896734.3018-34.4723
52.5183-0.840.74164.3797-0.70541.3406-0.09420.03690.26590.1915-0.03-0.219-0.31010.15980.05170.1592-0.0215-0.01070.0966-0.00430.13478.96445.2608-1.4556
61.63130.8386-0.68942.0159-0.9342.22480.0415-0.18850.07460.1295-0.03280.2072-0.1705-0.1419-0.01270.12580.03770.00310.1869-0.00780.1844-8.38020.19014.9934
70.8823-0.33610.57721.568-0.9452.364-0.0226-0.0997-0.1070.10350.09160.11460.0616-0.0984-0.060.10270.00440.02660.09890.00510.13350.8038-13.74416.8629
83.6856-4.00192.13594.5885-2.11251.4203-0.2303-0.8317-0.11630.57780.50750.2807-0.1481-0.2289-0.18890.30.05180.030.29630.06860.1908-0.4915-21.568425.9482
91.6927-0.09970.68761.0244-0.37821.83460.0126-0.0772-0.09050.06730.02110.12140.112-0.0729-0.02480.1271-0.00830.01970.09110.01170.1381-0.834-16.49815.9528
101.58350.1029-0.19434.87781.66972.88830.052-0.0921-0.21490.29810.0181-0.04450.437-0.0466-0.07920.1733-0.0008-0.00780.11340.01770.129414.3301-30.2538-5.293
113.09851.6797-0.06762.35180.33840.96570.05520.1183-0.29650.01730.1019-0.38770.04740.3028-0.13820.15390.0171-0.020.2264-0.06380.187328.4672-25.5929-15.3446
122.78231.33721.1641.59640.91562.00530.0147-0.04130.06990.04040.0329-0.0702-0.04150.1733-0.01950.08570.00810.01330.0979-0.01380.119525.9215-14.0291-5.6207
131.62570.3750.22890.80040.27781.19450.0148-0.02410.0790.00380.0672-0.1077-0.11540.2739-0.04670.1144-0.0222-0.0010.1363-0.02360.157429.977-7.5788-4.8862
142.82621.52431.55545.04040.69521.2457-0.21080.03940.3319-0.26760.05120.1305-0.3032-0.06280.08290.15820.0107-0.00620.10210.00030.1526-0.8563-30.0617-37.1899
153.5864-0.6385-1.38553.40812.46226.36650.05840.7282-0.0831-0.80980.0026-0.2162-0.3053-0.0416-0.09210.3032-0.01060.01940.2344-0.00460.178512.0997-32.0213-45.8144
160.9644-0.4106-0.56183.1691.72831.8865-0.02460.1924-0.2738-0.22090.1703-0.42770.04720.3131-0.13210.15270.0090.03030.2283-0.08180.25116.4351-43.9786-41.8072
170.83320.38070.36630.95530.56541.1678-0.02690.1797-0.1416-0.11230.1332-0.12820.09970.1146-0.07790.1553-0.00270.02050.1248-0.03450.13342.5303-52.0101-46.8308
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'D' and (resid 0 through 60 )D0 - 60
2X-RAY DIFFRACTION2chain 'D' and (resid 61 through 142 )D61 - 142
3X-RAY DIFFRACTION3chain 'D' and (resid 143 through 205 )D143 - 205
4X-RAY DIFFRACTION4chain 'D' and (resid 206 through 296 )D206 - 296
5X-RAY DIFFRACTION5chain 'A' and (resid -1 through 60 )A-1 - 60
6X-RAY DIFFRACTION6chain 'A' and (resid 61 through 142 )A61 - 142
7X-RAY DIFFRACTION7chain 'A' and (resid 143 through 237 )A143 - 237
8X-RAY DIFFRACTION8chain 'A' and (resid 238 through 254 )A238 - 254
9X-RAY DIFFRACTION9chain 'A' and (resid 255 through 296 )A255 - 296
10X-RAY DIFFRACTION10chain 'B' and (resid -1 through 53 )B-1 - 53
11X-RAY DIFFRACTION11chain 'B' and (resid 54 through 142 )B54 - 142
12X-RAY DIFFRACTION12chain 'B' and (resid 143 through 205 )B143 - 205
13X-RAY DIFFRACTION13chain 'B' and (resid 206 through 296 )B206 - 296
14X-RAY DIFFRACTION14chain 'C' and (resid -1 through 60 )C-1 - 60
15X-RAY DIFFRACTION15chain 'C' and (resid 61 through 95 )C61 - 95
16X-RAY DIFFRACTION16chain 'C' and (resid 96 through 142 )C96 - 142
17X-RAY DIFFRACTION17chain 'C' and (resid 143 through 296 )C143 - 296

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