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- PDB-4rfl: Crystal structure of G1PDH with NADPH from Methanocaldococcus jan... -

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Basic information

Entry
Database: PDB / ID: 4rfl
TitleCrystal structure of G1PDH with NADPH from Methanocaldococcus jannaschii
ComponentsGlycerol-1-phosphate dehydrogenase [NAD(P)+]
KeywordsOXIDOREDUCTASE / Rossman fold Metal Ion Binding / Dehydrogenase / NADP(H) binding / sn-glycerol-1-phosphate dehydrogenase
Function / homology
Function and homology information


glycerol-1-phosphate dehydrogenase [NAD+] activity / glycerol-1-phosphate dehydrogenase [NADP+] activity / sn-glycerol-1-phosphate dehydrogenase / glycerophospholipid metabolic process / phospholipid biosynthetic process / metal ion binding / cytoplasm
Similarity search - Function
Glycerol-1-phosphate dehydrogenase, archaea / Glycerol-1-phosphate dehydrogenase / Iron-containing alcohol dehydrogenase / Glycerol dehydrogenase / Dehydroquinate synthase-like, alpha domain / Dehydroquinate synthase-like - alpha domain / Rossmann fold - #1970 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich ...Glycerol-1-phosphate dehydrogenase, archaea / Glycerol-1-phosphate dehydrogenase / Iron-containing alcohol dehydrogenase / Glycerol dehydrogenase / Dehydroquinate synthase-like, alpha domain / Dehydroquinate synthase-like - alpha domain / Rossmann fold - #1970 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Chem-NDP / Glycerol-1-phosphate dehydrogenase [NAD(P)+]
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii DSM 2661 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCarbone, V. / Ronimus, R.S. / Schofield, L.R. / Sutherland-Smith, A.J.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structure and Evolution of the Archaeal Lipid Synthesis Enzyme sn-Glycerol-1-phosphate Dehydrogenase.
Authors: Carbone, V. / Schofield, L.R. / Zhang, Y. / Sang, C. / Dey, D. / Hannus, I.M. / Martin, W.F. / Sutherland-Smith, A.J. / Ronimus, R.S.
History
DepositionSep 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Database references
Revision 1.2Sep 16, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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 / _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: Glycerol-1-phosphate dehydrogenase [NAD(P)+]
B: Glycerol-1-phosphate dehydrogenase [NAD(P)+]
C: Glycerol-1-phosphate dehydrogenase [NAD(P)+]
D: Glycerol-1-phosphate dehydrogenase [NAD(P)+]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,20532
Polymers165,8514
Non-polymers4,35428
Water7,909439
1
A: Glycerol-1-phosphate dehydrogenase [NAD(P)+]
B: Glycerol-1-phosphate dehydrogenase [NAD(P)+]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,12216
Polymers82,9252
Non-polymers2,19614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7220 Å2
ΔGint-72 kcal/mol
Surface area27580 Å2
MethodPISA
2
C: Glycerol-1-phosphate dehydrogenase [NAD(P)+]
D: Glycerol-1-phosphate dehydrogenase [NAD(P)+]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,08316
Polymers82,9252
Non-polymers2,15714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7320 Å2
ΔGint-85 kcal/mol
Surface area27320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.391, 72.115, 101.714
Angle α, β, γ (deg.)77.62, 79.58, 75.63
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 0 / Auth seq-ID: 2 - 335 / Label seq-ID: 38 - 371

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Glycerol-1-phosphate dehydrogenase [NAD(P)+] / G1P dehydrogenase / G1PDH / Enantiomeric glycerophosphate synthase / sn-glycerol-1-phosphate dehydrogenase


Mass: 41462.711 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Gene: egsA, MJ0712 / Plasmid: pET100D / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3)
References: UniProt: Q58122, sn-glycerol-1-phosphate dehydrogenase

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Non-polymers , 6 types, 467 molecules

#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 439 / 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: 2.78 Å3/Da / Density % sol: 55.81 %
Crystal growTemperature: 294 K / pH: 8.5
Details: 30% (v/v) P550MME/P20K, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9116
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 27, 2013
RadiationMonochromator: SILICON DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9116 Å / Relative weight: 1
ReflectionResolution: 2.2→46.68 Å / Num. obs: 78703 / % possible obs: 98.3 % / Observed criterion σ(I): 0
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.827 / Mean I/σ(I) obs: 1.9 / % possible all: 95.8

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.8.0049refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CE9

3ce9


Resolution: 2.2→46.68 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / SU B: 7.164 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.253 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.225 4013 5 %RANDOM
Rwork0.185 ---
obs0.185 74699 98.3 %-
all-80009 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.53 Å2
Baniso -1Baniso -2Baniso -3
1--0.81 Å20.74 Å20.42 Å2
2--2.35 Å21.18 Å2
3----0.87 Å2
Refine analyzeLuzzati coordinate error obs: 0.269 Å
Refinement stepCycle: LAST / Resolution: 2.2→46.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10348 0 261 439 11048
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01910880
X-RAY DIFFRACTIONr_bond_other_d0.0030.0210767
X-RAY DIFFRACTIONr_angle_refined_deg1.5772.00814676
X-RAY DIFFRACTIONr_angle_other_deg2.726324905
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.14151342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.55324.673413
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.513152049
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8531548
X-RAY DIFFRACTIONr_chiral_restr0.0890.21700
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211794
X-RAY DIFFRACTIONr_gen_planes_other0.0220.022230
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_it2.4843.2625338
X-RAY DIFFRACTIONr_mcbond_other2.4833.2625337
X-RAY DIFFRACTIONr_mcangle_it3.6664.8796672
X-RAY DIFFRACTIONr_mcangle_other3.6664.8796673
X-RAY DIFFRACTIONr_scbond_it2.9143.6335542
X-RAY DIFFRACTIONr_scbond_other2.9143.6335542
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5355.3147999
X-RAY DIFFRACTIONr_long_range_B_refined5.90426.60412905
X-RAY DIFFRACTIONr_long_range_B_other5.90426.60312906
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)
11A209140.14
12B209140.14
21A208020.14
22C208020.14
31A204630.16
32D204630.16
41B205260.13
42C205260.13
51B207520.13
52D207520.13
61C203780.15
62D203780.15
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 289 -
Rwork0.275 5434 -
obs--95.81 %

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