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- PDB-5ui3: Crystal structure of DHDPS from chlamydomonas reinhardtii -

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Basic information

Entry
Database: PDB / ID: 5ui3
TitleCrystal structure of DHDPS from chlamydomonas reinhardtii
ComponentsDihydrodipicolinate synthase
KeywordsLYASE / DHDPS Lysine biosynthesis
Function / homology
Function and homology information


4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate
Similarity search - Function
4-hydroxy-tetrahydrodipicolinate synthase, DapA / Schiff base-forming aldolase, conserved site / Dihydrodipicolinate synthase signature 1. / Schiff base-forming aldolase, active site / Dihydrodipicolinate synthase signature 2. / DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase class I / Aldolase-type TIM barrel ...4-hydroxy-tetrahydrodipicolinate synthase, DapA / Schiff base-forming aldolase, conserved site / Dihydrodipicolinate synthase signature 1. / Schiff base-forming aldolase, active site / Dihydrodipicolinate synthase signature 2. / DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / 4-hydroxy-tetrahydrodipicolinate synthase
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsWatkin, S. / Keown, J.R. / Pearce, F.G.
CitationJournal: To Be Published
Title: Crystal structure of DHDPS from chlamydomonas reinhardtii
Authors: Watkin, S. / Keown, J.R. / Pearce, F.G.
History
DepositionJan 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _audit_author.name ..._audit_author.identifier_ORCID / _audit_author.name / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Dihydrodipicolinate synthase
A: Dihydrodipicolinate synthase
B: Dihydrodipicolinate synthase
C: Dihydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,5188
Polymers148,9334
Non-polymers5844
Water19,3121072
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10450 Å2
ΔGint-20 kcal/mol
Surface area39530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.700, 103.630, 78.130
Angle α, β, γ (deg.)90.000, 95.020, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21A
12D
22B
13D
23C
14A
24B
15A
25C
16B
26C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010D18 - 322
2010A18 - 322
1020D18 - 322
2020B18 - 322
1030D18 - 321
2030C18 - 321
1040A18 - 322
2040B18 - 322
1050A18 - 321
2050C18 - 321
1060B18 - 321
2060C18 - 321

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Dihydrodipicolinate synthase


Mass: 37233.332 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: DPS1, dapA, CHLREDRAFT_126518 / Production host: Escherichia coli (E. coli) / References: UniProt: A8I3W3
#2: Chemical
ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H6O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1072 / 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: 1.94 Å3/Da / Density % sol: 36.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 25% PEG 1500, 10% succinate-phosphate-glycine pH 5

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→62.23 Å / Num. obs: 73502 / % possible obs: 95.7 % / Redundancy: 6.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.13 / Net I/σ(I): 9.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2-2.045.60.7380.825198.6
9.8-62.236.10.0480.997198.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2 Å51.81 Å
Translation2 Å51.81 Å

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Processing

Software
NameVersionClassification
Aimless0.5.1data scaling
PHASER2.5.6phasing
REFMACrefinement
PDB_EXTRACT3.22data extraction
PHASERphasing
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→62.23 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.914 / SU B: 5.091 / SU ML: 0.135 / SU R Cruickshank DPI: 0.2529 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.253 / ESU R Free: 0.185
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2314 3542 4.8 %RANDOM
Rwork0.2014 ---
obs0.2028 69590 95.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 70.28 Å2 / Biso mean: 23.504 Å2 / Biso min: 11.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20 Å20.32 Å2
2--0.77 Å20 Å2
3----0.26 Å2
Refinement stepCycle: final / Resolution: 2→62.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9265 0 36 1072 10373
Biso mean--33.76 31.38 -
Num. residues----1221
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0199497
X-RAY DIFFRACTIONr_bond_other_d0.0020.028684
X-RAY DIFFRACTIONr_angle_refined_deg1.4391.94912866
X-RAY DIFFRACTIONr_angle_other_deg0.97320207
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.34251217
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.71524.693407
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.465151566
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8961544
X-RAY DIFFRACTIONr_chiral_restr0.0840.21445
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110643
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021789
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11D198560.05
12A198560.05
21D198400.05
22B198400.05
31D198880.04
32C198880.04
41A197800.05
42B197800.05
51A199180.04
52C199180.04
61B198840.04
62C198840.04
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 256 -
Rwork0.259 5285 -
all-5541 -
obs--98.23 %

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