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- PDB-1obf: The crystal structure of Glyceraldehyde 3-phosphate Dehydrogenase... -

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Basic information

Entry
Database: PDB / ID: 1obf
TitleThe crystal structure of Glyceraldehyde 3-phosphate Dehydrogenase from Alcaligenes xylosoxidans at 1.7A resolution.
ComponentsGLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE
KeywordsGLYCOLYTIC PATHWAY / OXIDOREDUCTASE / FREE-NAD GAPDH
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 / glucose metabolic process / NAD binding / NADP binding
Similarity search - Function
Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde-3-phosphate dehydrogenase, type I / 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, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde-3-phosphate dehydrogenase, type I / 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
Similarity search - Component
Biological speciesACHROMOBACTER XYLOSOXIDANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsAntonyuk, S.V. / Eady, R.R. / Strange, R.W. / Hasnain, S.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: The Structure of Glyceraldehyde 3-Phosphate Dehydrogenase from Alcaligenes Xylosoxidans at 1.7 A Resolution
Authors: Antonyuk, S.V. / Eady, R.R. / Strange, R.W. / Hasnain, S.S.
History
DepositionJan 30, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2003Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2014Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
O: GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE
P: GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2178
Polymers71,6572
Non-polymers5616
Water9,026501
1
O: GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE
P: GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE
hetero molecules

O: GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE
P: GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,43516
Polymers143,3144
Non-polymers1,12112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
MethodPQS
Unit cell
Length a, b, c (Å)88.984, 146.622, 146.622
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11O-2007-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.989, 0.003, -0.151), (-0.002, -0.999, -0.033), (-0.151, 0.033, -0.988)
Vector: 5.41295, 57.33633, 71.34437)

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Components

#1: Protein GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE


Mass: 35828.441 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ACHROMOBACTER XYLOSOXIDANS (bacteria)
References: UniProt: P83696*PLUS, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 501 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.3 Å3/Da / Density % sol: 59 %
Crystal growpH: 6.5
Details: PROTEIN 5MG/ML, 12 % PEG550, 100 MM POTASSIUM THIOCYANATE, 50 MM MES BUFFER (PH 6.5)
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mg/mlprotein1drop
212 %PEG5501drop
3100 mMpotassium thiocyanate1drop
450 mMMES1droppH6.5
524.5 %PEG5501reservoir
6200 mMpotassium thiocyanate1reservoir
7100 mMMES1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: May 15, 2001 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 102122 / % possible obs: 97.6 % / Redundancy: 6.7 % / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 22
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 6 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.2 / % possible all: 90.7
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 50 Å / Num. obs: 104690 / Redundancy: 6 % / Rmerge(I) obs: 0.099
Reflection shell
*PLUS
Highest resolution: 1.7 Å / % possible obs: 90.7 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.2

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GD1

1gd1


Resolution: 1.7→50 Å / SU B: 1.871 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.078 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18711 5007 5 %RANDOM
Rwork0.16594 ---
obs0.16701 96935 96.7 %-
Displacement parametersBiso mean: 23.299 Å2
Baniso -1Baniso -2Baniso -3
1--2.8 Å20 Å20 Å2
2---0.1 Å20 Å2
3---2.91 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5030 0 30 501 5561
Refinement
*PLUS
Lowest resolution: 50 Å / Rfactor Rfree: 0.189 / Rfactor Rwork: 0.168
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONbond_d0.0120.021
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.4971.948
X-RAY DIFFRACTIONplane_restr0.0050.02

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