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- PDB-4f3y: X-Ray Crystal Structure of Dihydrodipicolinate reductase from Bur... -

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Basic information

Entry
Database: PDB / ID: 4f3y
TitleX-Ray Crystal Structure of Dihydrodipicolinate reductase from Burkholderia thailandensis
ComponentsDihydrodipicolinate reductase4-hydroxy-tetrahydrodipicolinate reductase
KeywordsOXIDOREDUCTASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Dihydrodipicolinate reductase / NAD/NADH
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 / NAD binding / NADP binding / cytoplasm
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
4-hydroxy-tetrahydrodipicolinate reductase
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.
History
DepositionMay 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: 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 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.pdbx_dist_value / _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_ref_seq_dif.details / _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
B: Dihydrodipicolinate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,23117
Polymers57,0912
Non-polymers14015
Water4,774265
1
A: Dihydrodipicolinate reductase
B: Dihydrodipicolinate reductase
hetero molecules

A: Dihydrodipicolinate reductase
B: Dihydrodipicolinate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,46234
Polymers114,1824
Non-polymers28030
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_456-x-1,y,-z+11
Buried area14170 Å2
ΔGint-138 kcal/mol
Surface area39810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.740, 158.370, 70.440
Angle α, β, γ (deg.)90.00, 130.00, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-414-

HOH

21A-489-

HOH

DetailsUNKNOWN

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Components

#1: Protein Dihydrodipicolinate reductase / 4-hydroxy-tetrahydrodipicolinate reductase / DHPR


Mass: 28545.506 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / ATCC 700388 / DSM 13276 / CIP 106301 / Gene: BTH_I1208, dapB / Production host: Escherichia coli (E. coli) / References: UniProt: Q2SZ94, EC: 1.3.1.26
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 10 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.61 Å3/Da / Density % sol: 52.87 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.06M Magnesium chloride, 0.06M Calcium chloride, 0.10M Imidazole, 0.10M MES, 30% PEG550MME, 30% PEG20,000, ButhA.00820.a PW.33405 28.89mg/ml, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 1, 2012
RadiationMonochromator: Rigaku Varimax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 34301 / Num. obs: 33386 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 34.431 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 25.81
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.1-2.150.3576.01153932401195.3
2.15-2.210.4695.07168332277192
2.21-2.280.22411.47172592321196.2
2.28-2.350.278.52161812155192.4
2.35-2.420.20310.92164992183198.2
2.42-2.510.16712.99163242157198.4
2.51-2.60.15313.64158052081198.5
2.6-2.710.13815.32150081979198.3
2.71-2.830.10119.66146741928199
2.83-2.970.08322.37140461847198.9
2.97-3.130.06727.1133401747198.9
3.13-3.320.04835.55126821663198.8
3.32-3.550.03942.94117961547199.1
3.55-3.830.03651.51110341463199.1
3.83-4.20.0356.76101931339199
4.2-4.70.02764.4793031223198.7
4.7-5.420.02860.9382441077198.8
5.42-6.640.03155.066898901198.8
6.64-9.390.02369.985296701198.7
9.39-500.02184.282858396195.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1ARZ

1arz


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.924 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 9.66 / SU ML: 0.133 / Isotropic thermal model: Isotropic/TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.217 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2375 1688 5.1 %RANDOM
Rwork0.1898 ---
all0.1922 34301 --
obs0.1922 33385 98.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.25 Å2 / Biso mean: 32.053 Å2 / Biso min: 8.63 Å2
Baniso -1Baniso -2Baniso -3
1-3.12 Å20 Å21.87 Å2
2---1.27 Å20 Å2
3---0.56 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3868 0 15 265 4148
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193978
X-RAY DIFFRACTIONr_angle_refined_deg1.4611.9585387
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6115545
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.56222.901162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.22815639
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3931535
X-RAY DIFFRACTIONr_chiral_restr0.0910.2628
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023010
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 136 -
Rwork0.207 2241 -
all-2377 -
obs-2401 95.89 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.4954-0.3132-0.27044.6217-3.10824.6872-0.0249-0.0323-0.10610.10160.38310.74870.1753-0.42-0.35820.0699-0.02740.0720.05240.03250.1723-50.9165-39.545617.801
22.4268-0.0534-0.19595.2274-2.53462.8132-0.0077-0.0444-0.15830.2991-0.2577-0.40610.03460.2260.26540.10390.01150.0010.06160.02250.0507-37.2129-37.564116.4052
30.93250.3774-0.50812.46360.0441.49260.0115-0.13890.0296-0.1659-0.0156-0.59360.07480.42590.00410.04310.03640.0410.1340.01330.1885-40.4888-8.280623.7336
40.86350.353-0.81342.8079-0.07161.36820.0447-0.1781-0.02410.0584-0.0391-0.53570.03480.3245-0.00560.01570.0032-0.00290.1007-0.0170.1367-44.6336-3.75729.6911
52.4971-1.2123-3.23113.9749-1.2967.450.22380.00230.1833-0.0978-0.08570.1344-0.28240.1405-0.13810.0670.00250.02120.01580.01580.1244-41.1886-25.050310.4094
63.4406-1.3355-1.40385.33430.58994.2437-0.1401-0.02530.20770.26910.20330.2967-0.015-0.1935-0.06320.08010.01770.05280.020.01880.1225-48.181829.116718.9392
72.39821.0689-1.34214.34541.814.57940.2308-0.03520.63230.0380.06370.2795-0.6786-0.0165-0.29450.14620.02510.07710.03810.03740.2626-46.636135.261417.4164
84.5261-0.9373-2.31966.39591.06265.2943-0.08860.8039-0.0083-1.01780.13520.91160.1723-1.1356-0.04670.2471-0.0564-0.12790.34760.1110.1931-51.141924.86113.1327
90.7286-0.0707-0.45752.47560.39481.51240.07030.23530.1053-0.5418-0.00650.0939-0.0985-0.1989-0.06380.12640.0168-0.01450.07910.03660.0333-59.856-3.826612.0865
106.53281.8353-4.34713.4936-2.3844.5633-0.44380.3674-0.2427-0.4010.19440.06230.6778-0.27730.24940.2046-0.05760.06740.0322-0.01770.0472-44.168215.04038.091
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 51
2X-RAY DIFFRACTION2A52 - 124
3X-RAY DIFFRACTION3A125 - 184
4X-RAY DIFFRACTION4A185 - 236
5X-RAY DIFFRACTION5A237 - 268
6X-RAY DIFFRACTION6B2 - 45
7X-RAY DIFFRACTION7B46 - 71
8X-RAY DIFFRACTION8B72 - 125
9X-RAY DIFFRACTION9B126 - 236
10X-RAY DIFFRACTION10B237 - 268

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