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- PDB-5wol: Crystal structure of dihydrodipicolinate reductase DapB from Coxi... -

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Basic information

Entry
Database: PDB / ID: 5wol
TitleCrystal structure of dihydrodipicolinate reductase DapB from Coxiella burnetii
Components4-hydroxy-tetrahydrodipicolinate reductase
KeywordsOXIDOREDUCTASE / amino acid biosynthesis / L-lysine biosynthesis / NADPH / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / NIAID / National Institute of Allergy and Infectious Diseases / BIOSYNTHETIC PROTEIN
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 / 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 / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
PYRIDINE-2-CARBOXYLIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Chem-PE3 / 4-hydroxy-tetrahydrodipicolinate reductase
Similarity search - Component
Biological speciesCoxiella burnetii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsStogios, P.J. / Wawrzak, Z. / Onopriyenko, O. / Grimshaw, S. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
CitationJournal: To Be Published
Title: Crystal structure of dihydrodipicolinate reductase DapB from Coxiella burnetii
Authors: Stogios, P.J.
History
DepositionAug 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-hydroxy-tetrahydrodipicolinate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0837
Polymers26,2661
Non-polymers1,8176
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.605, 78.795, 84.074
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-460-

HOH

21A-490-

HOH

31A-512-

HOH

41A-605-

HOH

51A-618-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 4-hydroxy-tetrahydrodipicolinate reductase / / HTPA reductase


Mass: 26266.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxiella burnetii (strain RSA 493 / Nine Mile phase I) (bacteria)
Strain: RSA 493 / Nine Mile phase I / Gene: dapB, CBU_1709 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL
References: UniProt: P24703, 4-hydroxy-tetrahydrodipicolinate reductase

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Non-polymers , 5 types, 233 molecules

#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-6PC / PYRIDINE-2-CARBOXYLIC ACID / PICOLINIC ACID / Picolinic acid


Mass: 123.109 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5NO2
#5: Chemical ChemComp-PE3 / 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL / POLYETHYLENE GLYCOL / Polyethylene glycol


Mass: 634.751 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H58O15
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.32 Å3/Da / Density % sol: 46.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2 M ammonium sulfate, 2% (w/v) PEG400, 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 27235 / % possible obs: 99.8 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.016 / Net I/σ(I): 44.96
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.706 / Mean I/σ(I) obs: 1.95 / Num. unique obs: 1309 / CC1/2: 0.74 / Rpim(I) all: 0.333 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX(dev_2733: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPSIMBADphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YL5

1yl5


Resolution: 1.7→28.746 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.43
RfactorNum. reflection% reflectionSelection details
Rfree0.2176 1273 4.92 %RANDOM
Rwork0.1777 ---
obs0.1797 25853 94.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→28.746 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1757 0 86 227 2070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131920
X-RAY DIFFRACTIONf_angle_d1.272607
X-RAY DIFFRACTIONf_dihedral_angle_d20.405741
X-RAY DIFFRACTIONf_chiral_restr0.084300
X-RAY DIFFRACTIONf_plane_restr0.007329
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6996-1.76760.23861070.2131841X-RAY DIFFRACTION65
1.7676-1.8480.2353990.20222568X-RAY DIFFRACTION89
1.848-1.94540.27171570.20732816X-RAY DIFFRACTION99
1.9454-2.06730.21291720.1822831X-RAY DIFFRACTION100
2.0673-2.22690.20451650.17312827X-RAY DIFFRACTION100
2.2269-2.45080.21491580.17432862X-RAY DIFFRACTION100
2.4508-2.80520.21051210.17552904X-RAY DIFFRACTION100
2.8052-3.53330.20161180.17162940X-RAY DIFFRACTION100
3.5333-28.75020.21631760.16752991X-RAY DIFFRACTION99
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)
10.5883-0.4094-0.42571.11730.43690.85110.17720.14180.1293-0.1956-0.0867-0.0226-0.2431-0.10660.06960.39140.1120.15670.1831-0.01640.24319.3977-7.54089.9703
20.8194-0.5524-0.4850.52920.34350.28780.0170.1372-0.1413-0.1718-0.0235-0.20730.20240.27330.05460.1930.08480.11210.271-0.07960.265826.2646-12.590922.3274
31.03720.15180.15450.61840.22210.55980.0491-0.0039-0.13430.03270.0432-0.17510.10440.1841-0.06240.02840.0583-0.04230.0783-0.03910.07712.7944-11.234939.3109
40.9565-0.23280.98840.6478-0.25121.71410.0514-0.022-0.07940.0355-0.0009-0.0510.12810.0708-0.09880.03680.0357-0.06180.0351-0.0140.03325.4415-13.126340.659
50.7557-0.2595-0.3920.61550.08170.83160.13460.12630.0358-0.2520.0446-0.3162-0.0570.16890.10170.11940.02190.07980.1558-0.10040.190618.2904-2.504327.7894
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:79)
2X-RAY DIFFRACTION2(chain A and resid 80:113)
3X-RAY DIFFRACTION3(chain A and resid 114:157)
4X-RAY DIFFRACTION4(chain A and resid 158:198)
5X-RAY DIFFRACTION5(chain A and resid 199:239)

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