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- PDB-5u5i: The dimeric crystal structure of the selenomethionine derivative ... -

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Basic information

Entry
Database: PDB / ID: 5u5i
TitleThe dimeric crystal structure of the selenomethionine derivative of HTPA Reductase from Sellaginella moellendorffii
ComponentsHTPA Reductase
KeywordsOXIDOREDUCTASE / DHDPR / Dihydrodipicolinate reductase / HTPA reductase
Function / homology
Function and homology information


4-hydroxy-tetrahydrodipicolinate reductase / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / chloroplast stroma / NADPH binding
Similarity search - Function
Dihydrodipicolinate reductase, plant-type / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Dihydrodipicolinate reductase C-terminal domain-containing protein
Similarity search - Component
Biological speciesSelaginella moellendorffii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsKeown, J.R. / Goldstone, D.C. / Pearce, F.G.
CitationJournal: Biochem. J. / Year: 2018
Title: Plant DHDPR forms a dimer with unique secondary structure features that preclude higher-order assembly.
Authors: Watkin, S.A.J. / Keown, J.R. / Richards, E. / Goldstone, D.C. / Devenish, S.R.A. / Grant Pearce, F.
History
DepositionDec 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HTPA Reductase
B: HTPA Reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5945
Polymers61,2272
Non-polymers1,3673
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5520 Å2
ΔGint-35 kcal/mol
Surface area23320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.922, 64.676, 151.957
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HTPA Reductase


Mass: 30613.707 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Selaginella moellendorffii (plant) / Gene: SELMODRAFT_168311 / Production host: Escherichia coli (E. coli) / References: UniProt: D8R6G2
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.57 Å3/Da / Density % sol: 52.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.2 M CaCl2, 20 % w/v PEG3350

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9724 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 2.2→48.91 Å / Num. obs: 32763 / % possible obs: 99.9 % / Redundancy: 14.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.046 / Rrim(I) all: 0.176 / Net I/σ(I): 14.5 / Num. measured all: 480765 / Scaling rejects: 54
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.2-2.2714.91.4264166527910.770.3781.4762.599.6
9.07-48.9112.60.0569005480.9990.0140.05241.199.5

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0158refinement
Aimless0.5.15data scaling
SHELXDEphasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→48.91 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.922 / WRfactor Rfree: 0.2194 / WRfactor Rwork: 0.1789 / FOM work R set: 0.8064 / SU B: 12.794 / SU ML: 0.174 / SU R Cruickshank DPI: 0.2592 / SU Rfree: 0.207 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.259 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2446 1658 5.1 %RANDOM
Rwork0.2004 ---
obs0.2027 31055 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 128.37 Å2 / Biso mean: 41.426 Å2 / Biso min: 10.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å2-0 Å20 Å2
2--0.32 Å2-0 Å2
3---0.14 Å2
Refinement stepCycle: final / Resolution: 2.2→48.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4138 0 89 195 4422
Biso mean--25.7 36.19 -
Num. residues----550
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194317
X-RAY DIFFRACTIONr_bond_other_d0.0020.024026
X-RAY DIFFRACTIONr_angle_refined_deg1.3832.0055867
X-RAY DIFFRACTIONr_angle_other_deg0.89439314
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6655553
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.51524.407177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.26915655
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5571526
X-RAY DIFFRACTIONr_chiral_restr0.0690.2681
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214815
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02853
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 120 -
Rwork0.27 2243 -
all-2363 -
obs--99.49 %
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)
15.30092.20980.3185.66083.20279.3175-0.17870.160.29-0.15210.08530.0051-0.3484-0.17420.09340.2688-0.0292-0.09030.19330.01790.045238.07942.92611.224
22.73833.3094-0.221211.9201-0.38477.1045-0.64050.72380.5388-1.40620.10780.396-0.748-0.09560.53260.4192-0.0324-0.19880.37870.1210.176336.21546.793.349
34.03170.31492.53583.75492.85883.9232-0.51210.96670.2018-0.32310.364-0.1801-0.97211.06520.14810.6038-0.3258-0.17250.530.12570.083950.60951.74913.012
43.9891-0.39913.38821.1-1.05873.40030.22910.5513-0.0684-0.5325-0.3026-0.15490.4780.74260.07340.48110.05720.01450.45530.04210.042657.91539.84339.366
510.77187.18027.851410.45523.73988.30131.03020.786-0.9644-1.2027-0.4835-0.13211.53631.0029-0.54671.00030.5002-0.19620.6033-0.16410.176759.70129.20332.688
62.1689-0.62333.29931.0038-2.40457.61950.020.21330.0863-0.150.04420.0950.21170.1697-0.06420.342-0.0157-0.09640.2191-0.02390.053748.12443.10331.089
713.39344.2461-1.533811.1952.04446.8709-0.05820.18970.2261-0.33620.0097-0.2220.23860.48010.04850.15330.04290.00450.19270.02490.017963.08738.8672.217
83.4612-0.73210.3482.4481-0.8333.3447-0.0651-0.3180.2630.31820.0414-0.0644-0.428-0.07880.02370.1555-0.01790.00920.2028-0.03670.023159.0646.4475.75
92.335-1.99552.43662.9997-2.54252.7130.1953-0.2863-0.10390.02780.0550.48230.1054-0.2572-0.25030.3603-0.10940.0160.3334-0.01720.129847.18841.04647.613
106.394-0.38124.29486.1484-1.9129.27780.0376-0.7705-0.23580.38160.31461.04360.0569-1.5131-0.35220.2304-0.04520.07090.46870.05590.201239.54941.26550.949
111.116-0.35422.54911.902-0.68296.55910.3828-0.3262-0.2883-0.250.1560.49661.2335-0.7077-0.53880.3833-0.1182-0.0760.24650.0840.179449.65931.26353.342
123.12210.49841.75254.96211.224913.0935-0.06790.21230.107-0.40770.1934-0.4503-0.51791.0123-0.12550.3502-0.12610.02950.29890.02560.093565.35253.2659.947
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 53
2X-RAY DIFFRACTION2A54 - 80
3X-RAY DIFFRACTION3A81 - 137
4X-RAY DIFFRACTION4A138 - 171
5X-RAY DIFFRACTION5A172 - 219
6X-RAY DIFFRACTION6A220 - 288
7X-RAY DIFFRACTION7B11 - 31
8X-RAY DIFFRACTION8B32 - 137
9X-RAY DIFFRACTION9B138 - 174
10X-RAY DIFFRACTION10B175 - 202
11X-RAY DIFFRACTION11B203 - 262
12X-RAY DIFFRACTION12B263 - 288

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