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- PDB-5u5n: The dimeric crystal structure of HTPA Reductase from Sellaginella... -

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Basic information

Entry
Database: PDB / ID: 5u5n
TitleThe dimeric crystal structure 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 / chloroplast stroma / lysine biosynthetic process via diaminopimelate / 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 / MOLECULAR REPLACEMENT / Resolution: 2.1 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
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 / refine_hist / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)61,9495
Polymers60,5822
Non-polymers1,3673
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-35 kcal/mol
Surface area23750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.358, 61.746, 151.408
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 0 / Auth seq-ID: 11 - 286 / Label seq-ID: 2 - 277

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein HTPA Reductase


Mass: 30290.787 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 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.21 Å3/Da / Density % sol: 44.42 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.2 M MgCl2, 25% PEG 3350, 0.1 M BTP pH 5.5

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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: Jun 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.1→61.75 Å / Num. obs: 32251 / % possible obs: 100 % / Redundancy: 18.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.215 / Rpim(I) all: 0.051 / Rrim(I) all: 0.221 / Net I/σ(I): 11.7 / Num. measured all: 595927 / Scaling rejects: 1154
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
2.1-2.1613.12.0783374325830.4960.5942.1641.499.6
8.91-61.7516.60.05484625100.9990.0130.05535.899.9

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Processing

Software
NameVersionClassification
REFMACrefinement
Aimless0.5.15data scaling
PDB_EXTRACT3.22data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5U5I

5u5i


Resolution: 2.1→61.75 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.9 / WRfactor Rfree: 0.2413 / WRfactor Rwork: 0.1941 / FOM work R set: 0.6957 / SU B: 20.101 / SU ML: 0.247 / SU R Cruickshank DPI: 0.282 / SU Rfree: 0.2261 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.282 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2779 1646 5.1 %RANDOM
Rwork0.2246 ---
obs0.2274 30538 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.59 Å2 / Biso mean: 41.225 Å2 / Biso min: 22.08 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å2-0 Å2-0 Å2
2---0.75 Å20 Å2
3---1.05 Å2
Refinement stepCycle: final / Resolution: 2.1→61.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4181 0 89 144 4414
Biso mean--43.59 39.18 -
Num. residues----556
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0194359
X-RAY DIFFRACTIONr_bond_other_d0.0020.024088
X-RAY DIFFRACTIONr_angle_refined_deg1.6831.9925922
X-RAY DIFFRACTIONr_angle_other_deg0.98339464
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8695558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.21124.483174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.04815722
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.8481524
X-RAY DIFFRACTIONr_chiral_restr0.0940.2689
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214852
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02854
Refine LS restraints NCS

Ens-ID: 1 / Number: 16486 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.1→2.155 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 107 -
Rwork0.343 2206 -
all-2313 -
obs--99.61 %
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)
16.1232-1.7302-2.14852.87751.52245.6904-0.001-0.0165-0.22940.0549-0.06120.13770.1278-0.07630.06220.3871-0.02670.01970.14820.01360.0198-4.0289-11.007725.231
210.23830.1345-1.60023.08921.25043.9494-0.0301-1.0416-0.33270.49680.0228-0.00450.12890.32460.00730.57190.03620.00220.3320.05930.0551-2.1727-11.637534.977
37.0525-0.3582-2.5451.2898-1.09032.1185-0.0176-0.48150.91770.71230.086-0.297-0.59210.1078-0.06840.63440.0478-0.08430.2304-0.10150.18762.10820.290228.5187
42.9543-2.5737-1.90938.11150.59464.30580.28570.12691.42520.4699-0.1259-0.7722-0.7063-0.0802-0.15970.58650.01540.06820.12040.04560.97544.48365.957322.0288
52.89512.8135-2.26612.1261-9.18779.0245-0.1833-0.40110.14760.05290.0486-0.1241-0.75110.08750.13470.42920.0219-0.02480.3194-0.02480.057-2.13564.60662.3974
63.66021.0617-2.16893.0644-1.15523.15420.0087-0.5523-0.05170.2527-0.19290.1567-0.83360.07420.18420.75980.0444-0.02810.2501-0.04310.0368-12.8911.97850.595
73.57832.9497-2.99998.9106-5.389217.9379-0.0454-0.1752-0.0039-0.03730.0695-0.1383-0.24330.4305-0.02410.36-0.0125-0.00450.2292-0.07960.2674-7.19714.19810.9675
81.4186-0.56062.37771.9106-0.78574.0052-0.1183-0.23570.0132-0.07760.08870.1052-0.2631-0.38030.02960.54480.02650.03690.2414-0.00430.0114-8.94761.50326.7686
96.77740.6215-1.36178.3459-0.61854.94790.16210.22970.29290.35230.08060.3245-0.09610.0238-0.24270.45770.0574-0.01720.16110.0070.0326-5.331715.0088-35.1084
107.57243.58043.5693.4361.07251.9838-0.06810.9776-0.0031-0.54040.16240.06930.11430.4181-0.09430.5970.1098-0.01020.47850.05580.0983-2.659614.915-44.8302
115.0381.2952.53447.37940.33723.15090.27330.1402-0.7615-0.1611-0.2055-0.77540.22350.3755-0.06770.44870.0034-0.05090.21230.01240.21936.33624.9646-32.5185
126.1988-4.73876.46278.6581-9.694612.8367-0.316-0.00550.1220.7408-0.0524-0.1756-0.5830.36910.36830.5645-0.1027-0.07410.1864-0.00320.1113-2.19924.3439-12.1894
136.9513-0.44753.51882.4944-0.3844.0154-0.11380.6869-0.2036-0.53820.03070.3582-0.02090.76290.08310.5129-0.0468-0.01520.1908-0.00890.1141-7.6652-6.7253-10.2471
145.944-2.48674.07733.9184-1.5935.15640.07570.3383-0.6329-0.34480.08690.5371-0.09760.1299-0.16260.4549-0.0437-0.00010.1317-0.03620.1292-13.4878-5.8838-15.1815
151.70020.6482-2.14351.9978-2.33374.35420.1019-0.2343-0.06260.1663-0.2044-0.0369-0.58490.3740.10260.7337-0.0677-0.070.1682-0.01120.0174-1.38238.1425-16.3756
166.465710.48444.062717.01086.60022.5687-0.5549-0.1451.1014-0.9683-0.18081.8172-0.4334-0.03160.73581.1531-0.1411-0.25470.63350.05760.35081.11918.6549-16.3382
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 49
2X-RAY DIFFRACTION2A50 - 83
3X-RAY DIFFRACTION3A84 - 110
4X-RAY DIFFRACTION4A111 - 137
5X-RAY DIFFRACTION5A138 - 154
6X-RAY DIFFRACTION6A155 - 178
7X-RAY DIFFRACTION7A179 - 194
8X-RAY DIFFRACTION8A195 - 288
9X-RAY DIFFRACTION9B11 - 49
10X-RAY DIFFRACTION10B50 - 82
11X-RAY DIFFRACTION11B83 - 136
12X-RAY DIFFRACTION12B137 - 152
13X-RAY DIFFRACTION13B153 - 178
14X-RAY DIFFRACTION14B179 - 230
15X-RAY DIFFRACTION15B231 - 282
16X-RAY DIFFRACTION16B283 - 287

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