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- PDB-6gpj: Crystal structure of human GDP-D-mannose 4,6-dehydratase in compl... -

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Basic information

Entry
Database: PDB / ID: 6gpj
TitleCrystal structure of human GDP-D-mannose 4,6-dehydratase in complex with GDP-4F-Man
ComponentsGDP-mannose 4,6 dehydratase
KeywordsLYASE / GDP-mannose 4 / 6 dehydratase / fucosylation / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


GDP-L-fucose biosynthetic process / GDP-fucose biosynthesis / GDP-mannose 4,6-dehydratase / GDP-mannose 4,6-dehydratase activity / GDP-mannose metabolic process / 'de novo' GDP-L-fucose biosynthetic process / NADP+ binding / Notch signaling pathway / extracellular exosome / identical protein binding ...GDP-L-fucose biosynthetic process / GDP-fucose biosynthesis / GDP-mannose 4,6-dehydratase / GDP-mannose 4,6-dehydratase activity / GDP-mannose metabolic process / 'de novo' GDP-L-fucose biosynthetic process / NADP+ binding / Notch signaling pathway / extracellular exosome / identical protein binding / cytosol / cytoplasm
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
CITRIC ACID / Chem-G4F / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / GDP-mannose 4,6 dehydratase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.94 Å
AuthorsPfeiffer, M. / Krojer, T. / Johansson, C. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Nidetzky, B. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: Acs Catalysis / Year: 2019
Title: A Parsimonious Mechanism of Sugar Dehydration by Human GDP-Mannose-4,6-dehydratase.
Authors: Pfeiffer, M. / Johansson, C. / Krojer, T. / Kavanagh, K.L. / Oppermann, U. / Nidetzky, B.
History
DepositionJun 6, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 1.2Jan 17, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)166,13716
Polymers160,2264
Non-polymers5,91112
Water13,259736
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17580 Å2
ΔGint-48 kcal/mol
Surface area44870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.080, 114.438, 140.536
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12A
22C
13A
23B
14D
24C
15D
25B
16C
26B

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNAA23 - 3713 - 351
21ASNASNDB23 - 3713 - 351
12ALAALAAA23 - 3723 - 352
22ALAALACC23 - 3723 - 352
13ALAALAAA23 - 3723 - 352
23ALAALABD23 - 3723 - 352
14ASNASNDB23 - 3713 - 351
24ASNASNCC23 - 3713 - 351
15ASNASNDB23 - 3713 - 351
25ASNASNBD23 - 3713 - 351
16ALAALACC23 - 3723 - 352
26ALAALABD23 - 3723 - 352

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ADCB

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


Mass: 40056.465 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GMDS / Production host: Escherichia coli (E. coli) / References: UniProt: O60547, GDP-mannose 4,6-dehydratase

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Non-polymers , 5 types, 748 molecules

#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H8O7
#3: Chemical
ChemComp-G4F / [[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{S},6~{R})-5-fluoranyl-6-(hydroxymethyl)-3,4-bis(oxidanyl)oxan-2-yl] hydrogen phosphate


Mass: 607.332 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H24FN5O15P2
#4: 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
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 736 / 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: 2.38 Å3/Da / Density % sol: 48.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350 -- 0.2M ammonium citrate dibasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.94→63.91 Å / Num. obs: 110446 / % possible obs: 100 % / Redundancy: 6.5 % / Net I/σ(I): 5.8
Reflection shellResolution: 1.94→1.99 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 8103 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1T2A

1t2a


Resolution: 1.94→63.9 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.445 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23847 5308 4.8 %RANDOM
Rwork0.20967 ---
obs0.21104 104361 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.493 Å2
Baniso -1Baniso -2Baniso -3
1--0.81 Å20 Å20 Å2
2--1.82 Å2-0 Å2
3----1.01 Å2
Refinement stepCycle: 1 / Resolution: 1.94→63.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10832 0 382 736 11950
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01911502
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210308
X-RAY DIFFRACTIONr_angle_refined_deg1.4821.96515658
X-RAY DIFFRACTIONr_angle_other_deg0.944323852
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.03751365
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.70223.861531
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.972151858
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1051569
X-RAY DIFFRACTIONr_chiral_restr0.0830.21701
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212822
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022435
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.712.6925470
X-RAY DIFFRACTIONr_mcbond_other1.7092.6925469
X-RAY DIFFRACTIONr_mcangle_it2.5594.0276827
X-RAY DIFFRACTIONr_mcangle_other2.5594.0286828
X-RAY DIFFRACTIONr_scbond_it2.1172.8746032
X-RAY DIFFRACTIONr_scbond_other2.1132.8736030
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3044.2288829
X-RAY DIFFRACTIONr_long_range_B_refined4.69331.2212816
X-RAY DIFFRACTIONr_long_range_B_other4.68331.19112811
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A226100.04
12D226100.04
21A225080.06
22C225080.06
31A225240.05
32B225240.05
41D228020.05
42C228020.05
51D226620.06
52B226620.06
61C228440.05
62B228440.05
LS refinement shellResolution: 1.939→1.989 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 379 -
Rwork0.367 7542 -
obs--97.9 %

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