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- PDB-1kga: STRUCTURE OF 2-KETO-3-DEOXY-6-PHOSPHOGLUCONATE ALDOLASE AT 2.8 AN... -

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Entry
Database: PDB / ID: 1kga
TitleSTRUCTURE OF 2-KETO-3-DEOXY-6-PHOSPHOGLUCONATE ALDOLASE AT 2.8 ANGSTROMS RESOLUTION
Components2-KETO-3-DEOXY-6-PHOSPHOGLUCONATE ALDOLASE
KeywordsLYASE / LYASE (ALDEHYDE)
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 3.5 Å
AuthorsTulinsky, A.
Citation
Journal: J.Mol.Biol. / Year: 1982
Title: Structure of 2-keto-3-deoxy-6-phosphogluconate aldolase at 2 . 8 A resolution.
Authors: Mavridis, I.M. / Hatada, M.H. / Tulinsky, A. / Lebioda, L.
#1: Journal: J.Mol.Biol. / Year: 1982
Title: Comparison of the Folding of 2-Keto-3-Deoxy-6-Phosphogluconate Aldolase, Triosephosphate Isomerase and Pyruvate Kinase. Implications in Molecular Evolution
Authors: Lebioda, L. / Hatada, M.H. / Tulinsky, A. / Mavridis, I.M.
#2: Journal: Am.Cryst.Assoc.,Abstr.Papers (Winter Meeting) / Year: 1978
Title: The Folding and Structure of 2-Keto-3-Deoxy-6-Phosphogluconic Aldolase (Kdpg Aldolase) from Pseudomonas Putida, Interpreted in Light of the Amino Acid Sequence
Authors: Frentup, M. / Weber, L.D. / Tulinsky, A.
#3: Journal: Biochemistry / Year: 1976
Title: The Folding and Quaternary Structure of Trimeric 2-Keto-3-Deoxy-6-Phosphogluconic Aldolase at 3.5-Angstroms Resolution
Authors: Mavridis, I.M. / Tulinsky, A.
#4: Journal: J.Biol.Chem. / Year: 1973
Title: Confirmation of a Trimeric Subunit Arrangement for 2-Keto-3-Deoxy-6-Phosphogluconic Aldolase Using X-Ray Crystallographic Methods
Authors: Vandlen, R.L. / Ersfeld, D.L. / Tulinsky, A. / Wood, W.A.
History
DepositionAug 21, 1978Processing site: BNL
Revision 1.0Oct 13, 1978Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-KETO-3-DEOXY-6-PHOSPHOGLUCONATE ALDOLASE


Theoretical massNumber of molelcules
Total (without water)18,6561
Polymers18,6561
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.400, 103.400, 103.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1generate(-0.5, 0.866025), (-0.866025, -0.5), (1)118.94435, -21.68138
2generate(-0.5, -0.866025), (0.866025, -0.5), (1)40.65565, -113.87255

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Components

#1: Protein 2-KETO-3-DEOXY-6-PHOSPHOGLUCONATE ALDOLASE / Coordinate model: Cα atoms only


Mass: 18655.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / References: 2-dehydro-3-deoxy-phosphogluconate aldolase
Sequence detailsRECENT SEQUENCE INFORMATION FROM W.A.WOOD AND CO-WORKERS IMPLIES THE PRESENCE OF ABOUT 20 AMINO ...RECENT SEQUENCE INFORMATION FROM W.A.WOOD AND CO-WORKERS IMPLIES THE PRESENCE OF ABOUT 20 AMINO ACIDS IN ADDITION TO THOSE FOR WHICH COORDINATES ARE GIVEN IN THIS ENTRY. THESE RESIDUES MAY BE PRESENT AT THE CARBOXY TERMINUS OF THE CHAIN AS PRESENTED HERE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.94 Å3/Da / Density % sol: 75.09 %
Crystal grow
*PLUS
Method: other / Details: Vandlen, R.L., (1973) J. Biol. Chem., 248, 2251.

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

RefinementHighest resolution: 3.5 Å
Details: THE ORTHOGONAL AXIAL SYSTEM OF THIS ENTRY IS NOT THAT OF THE STANDARD REPRESENTATION OF THE SPACE GROUP P 21 3. THE *Z* AXIS OF THIS ENTRY IS PARALLEL TO A THREE-FOLD AXIS OF THE SPACE GROUP ...Details: THE ORTHOGONAL AXIAL SYSTEM OF THIS ENTRY IS NOT THAT OF THE STANDARD REPRESENTATION OF THE SPACE GROUP P 21 3. THE *Z* AXIS OF THIS ENTRY IS PARALLEL TO A THREE-FOLD AXIS OF THE SPACE GROUP AND CORRESPONDS TO A DIRECTION ALIGNED WITH A BODY DIAGONAL OF THE CONVENTIONAL CUBIC UNIT CELL. THIS TRIMER-FORMING AXIS PASSES THROUGH THE POINT X=53.2, Y=-45.2. THE TWO TRANSFORMATIONS GIVEN IN THE *MTRIX* RECORDS BELOW MAY BE USED TO GENERATE COORDINATES FOR THE REMAINING TWO SUBUNITS OF THE TRIMER IN THE COORDINATE SYSTEM OF THIS ENTRY. NOTE THAT THE THREE-FOLD AXIS INDICATED HERE IS A TRUE CRYSTALLOGRAPHIC SYMMETRY ELEMENT BUT IT IS EXPRESSED WITH RESPECT TO THE NON-STANDARD AXIAL SYSTEM.
Refinement stepCycle: LAST / Highest resolution: 3.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms173 0 0 0 173

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