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- PDB-1dih: THREE-DIMENSIONAL STRUCTURE OF E. COLI DIHYDRODIPICOLINATE REDUCTASE -

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Basic information

Entry
Database: PDB / ID: 1dih
TitleTHREE-DIMENSIONAL STRUCTURE OF E. COLI DIHYDRODIPICOLINATE REDUCTASE
ComponentsDIHYDRODIPICOLINATE REDUCTASE4-hydroxy-tetrahydrodipicolinate reductase
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


4-hydroxy-tetrahydrodipicolinate reductase / oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor / 4-hydroxy-tetrahydrodipicolinate reductase / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / amino acid biosynthetic process / NAD binding / NADP binding / identical protein binding / cytosol
Similarity search - Function
Dihydrodipicolinate reductase, conserved site / Dihydrodipicolinate reductase signature. / Dihydrodipicolinate reductase, C-terminal / Dihydrodipicolinate reductase / Dihydrodipicolinate reductase, C-terminus / Dihydrodipicolinate reductase, N-terminal / Dihydrodipicolinate reductase, N-terminus / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain ...Dihydrodipicolinate reductase, conserved site / Dihydrodipicolinate reductase signature. / Dihydrodipicolinate reductase, C-terminal / Dihydrodipicolinate reductase / Dihydrodipicolinate reductase, C-terminus / Dihydrodipicolinate reductase, N-terminal / Dihydrodipicolinate reductase, N-terminus / 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
Chem-NDP / 4-hydroxy-tetrahydrodipicolinate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsScapin, G. / Blanchard, J.S. / Sacchettini, J.C.
Citation
Journal: Biochemistry / Year: 1995
Title: Three-dimensional structure of Escherichia coli dihydrodipicolinate reductase.
Authors: Scapin, G. / Blanchard, J.S. / Sacchettini, J.C.
#1: Journal: Biochemistry / Year: 1995
Title: Expression, Purification and Characterization of E. Coli Dihydrodipicolinate Reductase
Authors: Reddy, S. / Sacchettini, J.C. / Blanchard, J.S.
History
DepositionSep 14, 1994Processing site: BNL
Revision 1.0Sep 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Other / Refinement description / Category: pdbx_database_status / software
Item: _pdbx_database_status.process_site / _software.classification
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DIHYDRODIPICOLINATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5392
Polymers28,7941
Non-polymers7451
Water1,06359
1
A: DIHYDRODIPICOLINATE REDUCTASE
hetero molecules

A: DIHYDRODIPICOLINATE REDUCTASE
hetero molecules

A: DIHYDRODIPICOLINATE REDUCTASE
hetero molecules

A: DIHYDRODIPICOLINATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,1568
Polymers115,1754
Non-polymers2,9824
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area16800 Å2
ΔGint-40 kcal/mol
Surface area41260 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)75.700, 81.200, 94.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Atom site foot note1: CIS PROLINE - PRO 167

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Components

#1: Protein DIHYDRODIPICOLINATE REDUCTASE / 4-hydroxy-tetrahydrodipicolinate reductase


Mass: 28793.631 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P04036, EC: 1.3.1.26
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51.06 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.2 Mammonium sulfate1reservoir
2100 mMHEPES1reservoir
318 mg/mlprotein1drop
42.2 Mammonium sulfate1drop
5100 mMHEPES1drop

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.1 Å / Num. obs: 15200 / % possible obs: 93.4 % / Observed criterion σ(I): 16 / Num. measured all: 76793 / Rmerge(I) obs: 0.077
Reflection shell
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 2.2 Å / % possible obs: 74.5 % / Num. unique obs: 2346 / Num. measured obs: 5854

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Processing

Software
NameClassification
X-PLORmodel building
TNTrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.2→20 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.187 --
obs-13459 89 %
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1979 0 48 59 2086
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.186 / Rfactor Rwork: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONt_bond_d
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_improper_angle_d
X-RAY DIFFRACTIONt_mcbond_it
X-RAY DIFFRACTIONt_scbond_it
X-RAY DIFFRACTIONt_mcangle_it
X-RAY DIFFRACTIONt_scangle_it

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