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- PDB-4rgq: Crystal structure of the Methanocaldococcus jannaschii G1PDH with... -

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Basic information

Entry
Database: PDB / ID: 4rgq
TitleCrystal structure of the Methanocaldococcus jannaschii G1PDH with NADPH and DHAP
ComponentsGlycerol-1-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / Dehydrogenase / Rossman fold / Metal Ion Binding / NADP(H) binding / Zn / sn-glycerol-1-phosphate dehydrogenase
Function / homology
Function and homology information


sn-glycerol-1-phosphate dehydrogenase / glycerol-1-phosphate dehydrogenase (NAD+) activity / glycerol-1-phosphate dehydrogenase (NADP+) activity / 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
1,3-DIHYDROXYACETONEPHOSPHATE / SN-GLYCEROL-1-PHOSPHATE / : / Chem-NDP / Glycerol-1-phosphate dehydrogenase [NAD(P)+]
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 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 30, 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 23, 2015Group: Database references
Revision 1.3Sep 30, 2015Group: Data collection
Revision 1.4Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Sep 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_alt_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_alt_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.pdbx_ptnr2_label_alt_id / _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
B: Glycerol-1-phosphate dehydrogenase
C: Glycerol-1-phosphate dehydrogenase
D: Glycerol-1-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,73139
Polymers164,4704
Non-polymers5,26135
Water8,359464
1
A: Glycerol-1-phosphate dehydrogenase
B: Glycerol-1-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,02222
Polymers82,2352
Non-polymers2,78720
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8860 Å2
ΔGint-64 kcal/mol
Surface area27190 Å2
MethodPISA
2
C: Glycerol-1-phosphate dehydrogenase
D: Glycerol-1-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,70917
Polymers82,2352
Non-polymers2,47415
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7730 Å2
ΔGint-79 kcal/mol
Surface area27890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.382, 71.898, 101.697
Angle α, β, γ (deg.)77.52, 79.54, 75.60
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: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEVALVALAA2 - 33435 - 367
21ILEILEVALVALBB2 - 33435 - 367
12ILEILEILEILEAA2 - 33535 - 368
22ILEILEILEILECC2 - 33535 - 368
13ILEILEILEILEAA2 - 33535 - 368
23ILEILEILEILEDD2 - 33535 - 368
14ILEILEILEILEBB2 - 33535 - 368
24ILEILEILEILECC2 - 33535 - 368
15METMETILEILEBB1 - 33534 - 368
25METMETILEILEDD1 - 33534 - 368
16ILEILEVALVALCC2 - 33435 - 367
26ILEILEVALVALDD2 - 33435 - 367

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 / G1P dehydrogenase / G1PDH / Enantiomeric glycerophosphate synthase / sn-glycerol-1-phosphate dehydrogenase


Mass: 41117.477 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Gene: egsA, MJ0712 / Plasmid: pET151D / 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 , 7 types, 499 molecules

#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-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-13P / 1,3-DIHYDROXYACETONEPHOSPHATE


Mass: 170.058 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H7O6P
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-1GP / SN-GLYCEROL-1-PHOSPHATE


Mass: 172.074 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9O6P
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 464 / 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: 2.47 Å3/Da / Density % sol: 50.28 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 30% (v/v) P550MME/P20K, 0.1 M hepes, pH 7.6, 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 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 26, 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: 2.22→46.66 Å / Num. all: 77389 / Num. obs: 76018 / % possible obs: 98.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2
Reflection shellResolution: 2.22→2.35 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 10895 / Rsym value: 0.778 / % possible all: 96.5

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Processing

Software
NameVersionClassification
Blu-Iceicedata collection
PHASERphasing
REFMAC5.8.0049refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4RFL

4rfl


Resolution: 2.23→46.66 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.931 / SU B: 7.635 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.269 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22865 3887 5 %RANDOM
Rwork0.1822 ---
all0.1822 77389 --
obs0.18452 71776 97.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.368 Å2
Baniso -1Baniso -2Baniso -3
1--1.71 Å21.03 Å20.16 Å2
2--2.99 Å21.97 Å2
3----0.42 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 2.23→46.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10366 0 316 464 11146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01910943
X-RAY DIFFRACTIONr_bond_other_d0.0030.0210830
X-RAY DIFFRACTIONr_angle_refined_deg1.5912.01114743
X-RAY DIFFRACTIONr_angle_other_deg2.761325051
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.33651341
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.26924.61410
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.961152056
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1921548
X-RAY DIFFRACTIONr_chiral_restr0.0910.21702
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211802
X-RAY DIFFRACTIONr_gen_planes_other0.0230.022234
X-RAY DIFFRACTIONr_mcbond_it2.6233.3835343
X-RAY DIFFRACTIONr_mcbond_other2.6233.3835342
X-RAY DIFFRACTIONr_mcangle_it3.9185.0616679
X-RAY DIFFRACTIONr_mcangle_other3.9185.0626680
X-RAY DIFFRACTIONr_scbond_it3.2333.8825600
X-RAY DIFFRACTIONr_scbond_other3.2333.8825600
X-RAY DIFFRACTIONr_scangle_other4.8695.6798061
X-RAY DIFFRACTIONr_long_range_B_refined6.82628.05213050
X-RAY DIFFRACTIONr_long_range_B_other6.82328.01112967
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A205780.14
12B205780.14
21A207450.13
22C207450.13
31A205930.14
32D205930.14
41B207920.14
42C207920.14
51B213370.12
52D213370.12
61C202140.14
62D202140.14
LS refinement shellResolution: 2.23→2.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 283 -
Rwork0.269 4902 -
obs-4902 89.88 %

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