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- PDB-2hki: Crystal structure of photosynthetic glyceraldehyde-3-phosphate de... -

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Basic information

Entry
Database: PDB / ID: 2hki
TitleCrystal structure of photosynthetic glyceraldehyde-3-phosphate dehydrogenase A4 isoform
ComponentsGlyceraldehyde-3-phosphate dehydrogenase A, chloroplast
KeywordsOXIDOREDUCTASE / rossmann fold / apo-form
Function / homology
Function and homology information


glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) activity / reductive pentose-phosphate cycle / apoplast / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / chloroplast / glucose metabolic process / NAD binding / NADP binding
Similarity search - Function
Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 ...Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsCamara-Artigas, A.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Crystallization and structural analysis of GADPH from Spinacia oleracea in a new form.
Authors: Camara-Artigas, A. / Hirasawa, M. / Knaff, D.B. / Wang, M. / Allen, J.P.
History
DepositionJul 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 30, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE UNP ENTRY G3PA_SPIOL DESCRIBES A GLN TO GLN-ALA CONFLICT IN THE FEATURES SECTION.

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplast
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6415
Polymers36,2561
Non-polymers3844
Water0
1
A: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplast
hetero molecules

A: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplast
hetero molecules

A: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplast
hetero molecules

A: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplast
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,56320
Polymers145,0264
Non-polymers1,53716
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_555y,x,-z1
Buried area17540 Å2
ΔGint-320 kcal/mol
Surface area45790 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)120.805, 120.805, 159.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Glyceraldehyde-3-phosphate dehydrogenase A, chloroplast / NADP-dependent glyceraldehydephosphate dehydrogenase subunit A


Mass: 36256.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach)
References: UniProt: P19866, glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating)
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4

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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: 4.02 Å3/Da / Density % sol: 69.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 2-5 % PEG 10,000, 0.4-0.6 M lithium sulphate or 0.8-1 M sodium chloride, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.008 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 3, 2001
Details: 58 CM LONG, PT-COATED,FUSED SILICA, VERTICAL FOCUSMIRROR
RadiationMonochromator: CYCLINDRICALLY BENT TRIANGULAR SI(111)ASYMMETRIC CUT,HORIZONTAL FOCUS
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 3→15 Å / Num. all: 12157 / Num. obs: 12035 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Biso Wilson estimate: 80.1 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.081 / Net I/σ(I): 20.1
Reflection shellResolution: 3→3.16 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 4.1 / Num. unique all: 1729 / Rsym value: 0.458 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RM4

1rm4


Resolution: 3→15 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.902 / SU B: 36.468 / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.888 / ESU R Free: 0.382 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26644 576 4.8 %RANDOM
Rwork0.20974 ---
all0.212 11522 --
obs0.21236 11522 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.196 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å20 Å20 Å2
2---0.82 Å20 Å2
3---1.64 Å2
Refinement stepCycle: LAST / Resolution: 3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2529 0 20 0 2549
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222587
X-RAY DIFFRACTIONr_angle_refined_deg1.4721.9643516
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.115334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.01624.51102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.85515439
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.591515
X-RAY DIFFRACTIONr_chiral_restr0.1010.2416
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021900
X-RAY DIFFRACTIONr_nbd_refined0.220.21171
X-RAY DIFFRACTIONr_nbtor_refined0.3150.21762
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.282
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.281
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.24
X-RAY DIFFRACTIONr_mcbond_it0.4681.51685
X-RAY DIFFRACTIONr_mcangle_it0.86722680
X-RAY DIFFRACTIONr_scbond_it1.0743999
X-RAY DIFFRACTIONr_scangle_it1.6984.5836
LS refinement shellResolution: 3→3.076 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 32 -
Rwork0.262 822 -
obs--100 %

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