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- PDB-1dru: ESCHERICHIA COLI DHPR/NADH COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1dru
TitleESCHERICHIA COLI DHPR/NADH COMPLEX
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 4-hydroxy-tetrahydrodipicolinate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsReddy, S.G. / Scapin, G. / Blanchard, J.S.
Citation
Journal: Biochemistry / Year: 1996
Title: Interaction of pyridine nucleotide substrates with Escherichia coli dihydrodipicolinate reductase: thermodynamic and structural analysis of binary complexes.
Authors: Reddy, S.G. / Scapin, G. / Blanchard, J.S.
#1: Journal: Biochemistry / Year: 1995
Title: Three-Dimensional Structure of Escherichia Coli Dihydrodipicolinate Reductase
Authors: Scapin, G. / Blanchard, J.S. / Sacchettini, J.C.
#2: Journal: Biochemistry / Year: 1995
Title: Expression, Purification, and Characterization of Escherichia Coli Dihydrodipicolinate Reductase
Authors: Reddy, S.G. / Sacchettini, J.C. / Blanchard, J.S.
History
DepositionJun 28, 1996Processing site: BNL
Revision 1.0Jan 27, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 3, 2024Group: 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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_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

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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)29,4572
Polymers28,7941
Non-polymers6631
Water1,13563
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)117,8288
Polymers115,1754
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area16180 Å2
ΔGint-63 kcal/mol
Surface area40390 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)81.200, 84.500, 91.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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


Mass: 28793.631 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: DAPB / Plasmid: PET3D / Gene (production host): DAPB / Production host: Escherichia coli (E. coli) / Strain (production host): BL213D / References: UniProt: P04036, EC: 1.3.1.26
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O

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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: 2.74 Å3/Da / Density % sol: 65 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Scapin, G., (1995) Biochemistry, 34, 3502.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12.2 Mammonium salfate1reservoir
2100 mMHEPES1reservoirpH7.5
318 mg/mlprotein1drop
42.2 Mammonium salfate1drop
5100 mMHEPES1drop
61.5-2.0 MNADPH1drop

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Sep 25, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 19014 / % possible obs: 77.1 % / Redundancy: 3.7 % / Rsym value: 0.076 / Net I/σ(I): 9.1
Reflection shellResolution: 1.9→2 Å / Redundancy: 1.54 % / Mean I/σ(I) obs: 1.5 / Rsym value: 0.296 / % possible all: 39.3
Reflection
*PLUS
Rmerge(I) obs: 0.076

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Processing

Software
NameClassification
AMoREphasing
TNTrefinement
XENGENdata reduction
XENGENdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DHPR-NADPH

Resolution: 2.2→20 Å / Isotropic thermal model: TNT BCORREL.DAT / σ(F): 2
Stereochemistry target values: ENGH AND HUBER MODIFIED FOR TNT
RfactorNum. reflection% reflection
obs0.192 13953 85 %
Solvent computationBsol: 693.6 Å2 / ksol: 1.22 e/Å3
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1974 0 44 63 2081
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01920813.5
X-RAY DIFFRACTIONt_angle_deg2.527662.5
X-RAY DIFFRACTIONt_dihedral_angle_d2012570
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.026493
X-RAY DIFFRACTIONt_gen_planes0.0293097
X-RAY DIFFRACTIONt_it4.43120810.4
X-RAY DIFFRACTIONt_nbd0.0911110
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Num. reflection all: 14276 / Rfactor all: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg200
X-RAY DIFFRACTIONt_planar_d0.0263
X-RAY DIFFRACTIONt_plane_restr0.0297

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