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- PDB-6x3b: Structure of RMD from Pseudomonas aeruginosa complexed with NADPH -

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Basic information

Entry
Database: PDB / ID: 6x3b
TitleStructure of RMD from Pseudomonas aeruginosa complexed with NADPH
ComponentsGDP-6-deoxy-D-mannose reductase
KeywordsOXIDOREDUCTASE / O-antigen / Lipopolysaccharide / GDP-rhamnose / NADPH / Pseudomonas
Function / homologyGDP-mannose 4,6-dehydratase activity / GDP-mannose 4,6 dehydratase / NAD(P)-binding domain / NAD(P)-binding domain superfamily / Chem-NDP / NITRATE ION / PYROPHOSPHATE 2- / GDP-6-deoxy-D-mannose reductase
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsCook, P.D. / Nicholson, B.E. / McHugh, C.S.
CitationJournal: To Be Published
Title: X-ray crystallographic structure of RMD, the reductase involved in GDP-d-rhamnose production
Authors: Nicholson, B.E. / McHugh, C.S. / Cook, P.D.
History
DepositionMay 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GDP-6-deoxy-D-mannose reductase
B: GDP-6-deoxy-D-mannose reductase
C: GDP-6-deoxy-D-mannose reductase
D: GDP-6-deoxy-D-mannose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,15011
Polymers145,1854
Non-polymers3,9657
Water9,458525
1
A: GDP-6-deoxy-D-mannose reductase
B: GDP-6-deoxy-D-mannose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3216
Polymers72,5922
Non-polymers1,7294
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-28 kcal/mol
Surface area25370 Å2
MethodPISA
2
C: GDP-6-deoxy-D-mannose reductase
D: GDP-6-deoxy-D-mannose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8295
Polymers72,5922
Non-polymers2,2363
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-36 kcal/mol
Surface area24210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.680, 54.050, 137.920
Angle α, β, γ (deg.)90.000, 107.700, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
GDP-6-deoxy-D-mannose reductase / NAD-dependent epimerase/dehydratase family protein


Mass: 36296.223 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: CGU42_28985, DZ962_06890, EQH76_14905, F3H14_30110 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A071L2P8
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#4: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 525 / Source method: isolated from a natural source / Formula: H2O
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: 2.39 Å3/Da / Density % sol: 48.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 10% PEG 3350, 100 mM lithium nitrate, 10 mM HEPES, 25 mM NaCl

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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-225 / Detector: CCD / Date: Jun 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.91→34.03 Å / Num. obs: 105890 / % possible obs: 99.1 % / Redundancy: 5 % / Biso Wilson estimate: 26.57 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.049 / Rrim(I) all: 0.111 / Net I/σ(I): 8.5 / Num. measured all: 534372 / Scaling rejects: 287
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.91-1.9450.9212610651780.6660.4511.0271.698.5
10.46-34.034.30.03229886880.9970.0170.03722.196

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Processing

Software
NameVersionClassification
Aimless0.1.26data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2pk3

2pk3


Resolution: 1.91→34.028 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2239 5274 4.99 %
Rwork0.1866 100495 -
obs0.1885 105769 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.68 Å2 / Biso mean: 35.3508 Å2 / Biso min: 11.9 Å2
Refinement stepCycle: final / Resolution: 1.91→34.028 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9092 0 253 525 9870
Biso mean--34.51 35.65 -
Num. residues----1177
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079624
X-RAY DIFFRACTIONf_angle_d0.84513164
X-RAY DIFFRACTIONf_chiral_restr0.0531483
X-RAY DIFFRACTIONf_plane_restr0.0051686
X-RAY DIFFRACTIONf_dihedral_angle_d5.0647182
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.91-1.93170.35431690.295334898
1.9317-1.95440.34451720.2691326098
1.9544-1.97830.3121730.2567329298
1.9783-2.00330.2771710.237335998
2.0033-2.02970.29571510.2288328298
2.0297-2.05750.27371640.2239331298
2.0575-2.08690.26911700.2247331898
2.0869-2.1180.26611480.2223332198
2.118-2.15110.29961850.2193332698
2.1511-2.18630.24271920.2047326499
2.1863-2.2240.24551450.198336299
2.224-2.26450.2421480.1989337399
2.2645-2.3080.22941930.1944328599
2.308-2.35510.24191980.1975331899
2.3551-2.40630.25061810.1873328199
2.4063-2.46230.21361660.1892343599
2.4623-2.52380.24311640.195329699
2.5238-2.59210.23391830.1968338599
2.5921-2.66830.22821690.1905332099
2.6683-2.75440.2061890.1831334499
2.7544-2.85280.24091900.1928337099
2.8528-2.96690.2311800.199334099
2.9669-3.10190.25451900.1992334999
3.1019-3.26530.2281990.1938335799
3.2653-3.46970.23321600.1877340999
3.4697-3.73730.20791940.17553379100
3.7373-4.11280.18981800.1603341099
4.1128-4.70660.17971810.14883398100
4.7066-5.92470.21421780.1643463100
5.9247-340.16881910.1629353999

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