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- PDB-1rpn: Crystal Structure of GDP-D-mannose 4,6-dehydratase in complexes w... -

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Basic information

Entry
Database: PDB / ID: 1rpn
TitleCrystal Structure of GDP-D-mannose 4,6-dehydratase in complexes with GDP and NADPH
ComponentsGDP-mannose 4,6-dehydratase
KeywordsLYASE / short-chain dehydrogenase/reductase / Rossmann fold
Function / homology
Function and homology information


GDP-D-rhamnose biosynthetic process / GDP-mannose 4,6-dehydratase / GDP-mannose 4,6-dehydratase activity / 'de novo' GDP-L-fucose biosynthetic process / O antigen biosynthetic process / lipopolysaccharide biosynthetic process / NADP+ binding
Similarity search - Function
GDP-mannose 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
GUANOSINE-5'-DIPHOSPHATE / Chem-NDP / GDP-mannose 4,6-dehydratase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsWebb, N.A. / Mulichak, A.M. / Lam, J.S. / Rocchetta, H.L. / Garavito, R.M.
CitationJournal: Protein Sci. / Year: 2004
Title: Crystal structure of a tetrameric GDP-D-mannose 4,6-dehydratase from a bacterial GDP-D-rhamnose biosynthetic pathway.
Authors: Webb, N.A. / Mulichak, A.M. / Lam, J.S. / Rocchetta, H.L. / Garavito, R.M.
History
DepositionDec 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 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

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Assembly

Deposited unit
A: GDP-mannose 4,6-dehydratase
B: GDP-mannose 4,6-dehydratase
C: GDP-mannose 4,6-dehydratase
D: GDP-mannose 4,6-dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,15412
Polymers151,3994
Non-polymers4,7548
Water12,484693
1
A: GDP-mannose 4,6-dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0383
Polymers37,8501
Non-polymers1,1892
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GDP-mannose 4,6-dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0383
Polymers37,8501
Non-polymers1,1892
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: GDP-mannose 4,6-dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0383
Polymers37,8501
Non-polymers1,1892
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: GDP-mannose 4,6-dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0383
Polymers37,8501
Non-polymers1,1892
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19600 Å2
ΔGint-81 kcal/mol
Surface area37400 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)125.730, 125.730, 220.025
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
GDP-mannose 4,6-dehydratase / GDP-D-mannose dehydratase


Mass: 37849.805 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: GCA, PA5453 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q51366, GDP-mannose 4,6-dehydratase
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 693 / 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: 3.31 Å3/Da / Density % sol: 62.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: MPD, Tris, ammonium phosphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 %MPD1reservoir
2100 mMTris1reservoirpH8.5
3200 mM1reservoirNH4H2PO4
420 mMTris1droppH8.5
51 mM1dropNaCl
610 mMprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 13, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. all: 110070 / Num. obs: 108095 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5 % / Rsym value: 0.039 / Net I/σ(I): 20
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 4 % / Num. unique all: 10063 / Rsym value: 0.079 / % possible all: 92.8
Reflection
*PLUS
Highest resolution: 2.2 Å / Rmerge(I) obs: 0.039
Reflection shell
*PLUS
% possible obs: 92.8 % / Rmerge(I) obs: 0.076

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1N7H

1n7h


Resolution: 2.15→30 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.196 5398 -random
Rwork0.174 ---
all0.176 109784 --
obs0.176 107124 97.6 %-
Displacement parametersBiso mean: 20.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å2-0.63 Å20 Å2
2--0.43 Å20 Å2
3----0.86 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 2.15→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10008 0 304 693 11005
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.7
Refinement
*PLUS
Highest resolution: 2.2 Å / Num. reflection obs: 110170 / % reflection Rfree: 4.9 % / Rfactor Rfree: 0.195 / Rfactor Rwork: 0.173
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.7

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