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- PDB-1drw: ESCHERICHIA COLI DHPR/NHDH COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1drw
TitleESCHERICHIA COLI DHPR/NHDH COMPLEX
ComponentsDIHYDRODIPICOLINATE 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 PURIN-6-OL-DINUCLEOTIDE / 4-hydroxy-tetrahydrodipicolinate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER / 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

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Assembly

Deposited unit
A: DIHYDRODIPICOLINATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4582
Polymers28,7941
Non-polymers6641
Water1,45981
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)117,8328
Polymers115,1754
Non-polymers2,6584
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 area16920 Å2
ΔGint-56 kcal/mol
Surface area41200 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)75.600, 81.700, 93.800
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 / 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-NHD / NICOTINAMIDE PURIN-6-OL-DINUCLEOTIDE


Mass: 664.410 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H26N6O15P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.63 Å3/Da / Density % sol: 62 %
Crystal growpH: 7.5 / Details: 2.2M (NH4)2SO4 IN 100 MM HEPES, 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: Dec 7, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 14125 / % possible obs: 74.3 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rsym value: 0.061 / Net I/σ(I): 9.9
Reflection shellResolution: 2→2.1 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.228 / % possible all: 30
Reflection
*PLUS
Rmerge(I) obs: 0.061

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Processing

Software
NameClassification
PHASESphasing
TNTrefinement
XENGENdata reduction
XENGENdata scaling
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: DHPR-NADPH COMPLEX

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
Rwork0.18 --
obs-12405 82 %
Solvent computationBsol: 374.9 Å2 / ksol: 0.85 e/Å3
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1980 0 44 81 2105
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0221052.5
X-RAY DIFFRACTIONt_angle_deg1.7727623
X-RAY DIFFRACTIONt_dihedral_angle_d20.712550
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.03492
X-RAY DIFFRACTIONt_gen_planes0.053083
X-RAY DIFFRACTIONt_it3.9321050.4
X-RAY DIFFRACTIONt_nbd0.0711510
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Num. reflection all: 12764 / Rfactor all: 0.185 / Rfactor obs: 0.18 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_angle_deg1.8
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg20.70
X-RAY DIFFRACTIONt_planar_d0.032
X-RAY DIFFRACTIONt_plane_restr0.053

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