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- PDB-6gg7: cyanobacterial GAPDH with full-length CP12 -

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Basic information

Entry
Database: PDB / ID: 6gg7
Titlecyanobacterial GAPDH with full-length CP12
Components
  • CP12 polypeptide
  • Glyceraldehyde-3-phosphate dehydrogenaseGlyceraldehyde 3-phosphate dehydrogenase
KeywordsPHOTOSYNTHESIS / Calvin Cycle / Regulation
Function / homology
Function and homology information


Oxidoreductases, Acting on the aldehyde or oxo group of donors, With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / NAD binding / glucose metabolic process / NADP binding / nucleotide binding
Glyceraldehyde 3-phosphate dehydrogenase, active site / NAD(P)-binding domain superfamily / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / CP12 domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Domain of unknown function CP12 / Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain ...Glyceraldehyde 3-phosphate dehydrogenase, active site / NAD(P)-binding domain superfamily / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / CP12 domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Domain of unknown function CP12 / Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Calvin cycle protein CP12-like / Glyceraldehyde/Erythrose phosphate dehydrogenase family
CP12 polypeptide / Glyceraldehyde-3-phosphate dehydrogenase
Biological speciesThermosynechococcus elongatus (Cyanobacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsMcFarlane, C.R. / Murray, J.W.
Funding supportUnited Kingdom , 1件
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/J014575/1United Kingdom
CitationJournal: To Be Published
Title: cyanobacterial GAPDH with full-length CP12
Authors: McFarlane, C.R. / Shah, N. / Bubeck, D. / Murray, J.W.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 2, 2018 / Release: May 8, 2019
RevisionDateData content typeProviderType
1.0May 8, 2019Structure modelrepositoryInitial release

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Structure visualization

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Assembly

Deposited unit
B: Glyceraldehyde-3-phosphate dehydrogenase
C: CP12 polypeptide
A: Glyceraldehyde-3-phosphate dehydrogenase
D: CP12 polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,1356
Polymers90,8084
Non-polymers1,3272
Water10,160564
1
B: Glyceraldehyde-3-phosphate dehydrogenase
C: CP12 polypeptide
A: Glyceraldehyde-3-phosphate dehydrogenase
D: CP12 polypeptide
hetero molecules

B: Glyceraldehyde-3-phosphate dehydrogenase
C: CP12 polypeptide
A: Glyceraldehyde-3-phosphate dehydrogenase
D: CP12 polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,26912
Polymers181,6158
Non-polymers2,6544
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area29220 Å2
ΔGint-162 kcal/mol
Surface area43110 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)141.052, 141.052, 75.931
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-1109-

HOH

21A-1126-

HOH

31A-1300-

HOH

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Components

#1: Protein/peptide Glyceraldehyde-3-phosphate dehydrogenase / Glyceraldehyde 3-phosphate dehydrogenase


Mass: 36792.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus (strain BP-1) (Cyanobacteria)
Strain: BP-1 / Gene: tll1466 / Plasmid: pRSETA modified / Details (production host): thrombin cleavable his-tag / Production host: Escherichia coli KRX (bacteria)
References: UniProt: Q8DIW5, Oxidoreductases, Acting on the aldehyde or oxo group of donors, With NAD+ or NADP+ as acceptor
#2: Protein/peptide CP12 polypeptide


Mass: 8611.127 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus (strain BP-1) (Cyanobacteria)
Strain: BP-1 / Gene: cp12 / Plasmid: pRSETA modified / Details (production host): thrombin cleavable his-tag / Production host: Escherichia coli KRX (bacteria) / References: UniProt: Q8DHX3
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Nicotinamide adenine dinucleotide / Comment: NAD *YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 564 / Source method: isolated from a natural source / Formula: H2O / Water

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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: 2.4 Å3/Da / Density % sol: 48.96 %
Crystal growTemperature: 290 K / Method: vapor diffusion
Details: Tryptone CM1(A6) 1% Tryptone, 25% PEG, 100 mM Hepes pH 8.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96861 Å / Relative weight: 1
ReflectionResolution: 1.32→60.42 Å / Num. obs: 178371 / % possible obs: 99.99 % / Redundancy: 12.8 % / Biso Wilson estimate: 13.62 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.1266 / Rrim(I) all: 0.132 / Net I/σ(I): 11.43
Reflection shellResolution: 1.32→1.367 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.9185 / Num. unique obs: 17624 / CC1/2: 0.586 / Rrim(I) all: 0.9573 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BOY
Resolution: 1.32→60.416 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.65
RfactorNum. reflection% reflection
Rfree0.1735 8791 4.93 %
Rwork0.1454 --
Obs0.1468 178371 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.32→60.416 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5516 0 88 564 6168
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealNumber
f_bond_d0.0055908
f_angle_d0.9218081
f_dihedral_angle_d13.5173333
f_chiral_restr0.078916
f_plane_restr0.0061049
LS refinement shell

Refinement-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.3197-1.33470.28353030.2611556399
1.3347-1.35040.27252970.25015539100
1.3504-1.36680.26832940.24325592100
1.3668-1.38410.26282940.22845611100
1.3841-1.40240.24952760.21325599100
1.4024-1.42160.2233270.18835553100
1.4216-1.44190.22442970.17885612100
1.4419-1.46340.21132810.17285592100
1.4634-1.48630.21323080.16325584100
1.4863-1.51060.17722730.15125633100
1.5106-1.53670.19352790.14595616100
1.5367-1.56460.17422440.1445625100
1.5646-1.59470.17882890.13555639100
1.5947-1.62730.172990.12725603100
1.6273-1.66270.16242910.12175623100
1.6627-1.70140.16313200.12365603100
1.7014-1.74390.16673030.11985627100
1.7439-1.79110.1423050.11765610100
1.7911-1.84380.16522900.11985646100
1.8438-1.90330.16242830.12285672100
1.9033-1.97130.15062930.12985633100
1.9713-2.05020.15362950.13055667100
2.0502-2.14360.15382630.12995671100
2.1436-2.25660.17232900.12815687100
2.2566-2.3980.16513050.13725684100
2.398-2.58310.1653000.1455707100
2.5831-2.84310.17253060.1495723100
2.8431-3.25440.17982810.15815769100
3.2544-4.10010.15912980.13685826100
4.1001-60.4790.16693070.14816071100

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