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Basic information

Entry
Database: PDB / ID: 7xdu
TitleTtherAmDH-NAD+
Components4-hydroxy-tetrahydrodipicolinate reductase
KeywordsOXIDOREDUCTASE / Complex
Function / homology
Function and homology information


4-hydroxy-tetrahydrodipicolinate reductase / lysine biosynthetic process via diaminopimelate / nucleotide binding
Similarity search - Function
2,4-diaminopentanoate dehydrogenase, C-terminal domain / 2,4-diaminopentanoate dehydrogenase C-terminal domain / Dihydrodipicolinate reductase, N-terminal / Dihydrodipicolinate reductase, N-terminus / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 4-hydroxy-tetrahydrodipicolinate reductase
Similarity search - Component
Biological speciesThermoanaerobacter thermohydrosulfuricus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsChen, C. / Qian, Y.Y. / Pan, J. / Bai, Y.P. / Xu, J.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971380 China
CitationJournal: To Be Published
Title: Stereoselective synthesis of chiral lactams via an engineered natural amine dehydrogenase.
Authors: Chen, C. / Qian, Y.Y. / Pan, J. / Xu, J.H. / Bai, Y.P.
History
DepositionMar 28, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)78,1624
Polymers76,8352
Non-polymers1,3272
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-36 kcal/mol
Surface area27320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)203.061, 54.845, 114.188
Angle α, β, γ (deg.)90.000, 115.560, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 4-hydroxy-tetrahydrodipicolinate reductase


Mass: 38417.344 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter thermohydrosulfuricus (bacteria)
Gene: SAMN04244560_00044, SAMN04324257_01069 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1I1Z0X1
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.73 Å3/Da / Density % sol: 67.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: sodium malonate dibasic onohydrate, Bis-Tris propane, PEG 3350 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 35169 / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.057 / Rrim(I) all: 0.149 / Χ2: 0.996 / Net I/σ(I): 6.8 / Num. measured all: 241862
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
2.6-2.647.10.35317090.9640.1420.3810.992
2.64-2.697.10.33917650.9670.1370.3661.09
2.69-2.7470.28517590.980.1160.3080.994
2.74-2.870.26816940.9770.1080.2890.998
2.8-2.8670.2417540.9810.0980.261.007
2.86-2.9370.22517650.9820.0920.2430.974
2.93-36.90.20417280.9830.0840.221.026
3-3.086.70.18517660.9810.0770.2010.988
3.08-3.176.30.17217410.9810.0740.1880.984
3.17-3.286.60.16317330.9820.0680.1770.991
3.28-3.3970.1517640.9850.0610.1620.972
3.39-3.537.20.13917390.9860.0560.150.984
3.53-3.697.10.13917590.9860.0560.151.005
3.69-3.887.10.13117570.9850.0530.1410.941
3.88-4.1370.12117460.9840.0490.1310.884
4.13-4.456.70.11617690.9860.0480.1250.871
4.45-4.896.30.11117840.9840.0470.120.863
4.89-5.670.11517800.9840.0460.1240.843
5.6-7.0570.11917950.9820.0490.1290.842
7.05-506.50.13918620.9490.0580.1511.677

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIX1.17_3644refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6G1M

6g1m


Resolution: 2.6→45.8 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2258 1728 5.08 %
Rwork0.1796 32318 -
obs0.182 34046 96.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.05 Å2 / Biso mean: 42.8694 Å2 / Biso min: 15.37 Å2
Refinement stepCycle: final / Resolution: 2.6→45.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5255 0 88 176 5519
Biso mean--40.34 42.93 -
Num. residues----694
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.680.32841100.23912184229479
2.68-2.770.29351250.22782454257988
2.77-2.870.28471210.2282613273495
2.87-2.980.30151600.22182740290099
2.98-3.120.32481330.23327652898100
3.12-3.280.28551570.217427692926100
3.28-3.490.2641380.191727792917100
3.49-3.750.19131310.175827882919100
3.75-4.130.20811640.161927622926100
4.13-4.730.16751690.14112781295099
4.73-5.960.21431590.157927992958100
5.96-45.80.18291610.15312884304599

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