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- PDB-8h50: Crystal structure of carboxyspermidine dehydrogenase from Helicob... -

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Basic information

Entry
Database: PDB / ID: 8h50
TitleCrystal structure of carboxyspermidine dehydrogenase from Helicobacter pylori in space group C2221
ComponentsSaccharopine dehydrogenase
KeywordsBIOSYNTHETIC PROTEIN / carboxyspermidine dehydrogenase
Function / homologySaccharopine dehydrogenase, NADP binding domain / Saccharopine dehydrogenase-like, C-terminal / Saccharopine dehydrogenase NADP binding domain / Saccharopine dehydrogenase C-terminal domain / NAD(P)-binding domain superfamily / Saccharopine dehydrogenase
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKo, K.Y. / Park, S.C. / Cho, S.Y. / Yoon, S.I.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2019R1A2C1002100 Korea, Republic Of
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Structural analysis of carboxyspermidine dehydrogenase from Helicobacter pylori.
Authors: Ko, K.Y. / Park, S.C. / Cho, S.Y. / Yoon, S.I.
History
DepositionOct 11, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Refinement description ...Database references / Refinement description / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / struct_ncs_dom_lim / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_gen.gene_src_strain ..._entity.pdbx_description / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _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 / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Revision 1.2Oct 25, 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: Saccharopine dehydrogenase
B: Saccharopine dehydrogenase
C: Saccharopine dehydrogenase


Theoretical massNumber of molelcules
Total (without water)137,6423
Polymers137,6423
Non-polymers00
Water724
1
A: Saccharopine dehydrogenase
B: Saccharopine dehydrogenase


Theoretical massNumber of molelcules
Total (without water)91,7612
Polymers91,7612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-23 kcal/mol
Surface area31550 Å2
MethodPISA
2
C: Saccharopine dehydrogenase

C: Saccharopine dehydrogenase


Theoretical massNumber of molelcules
Total (without water)91,7612
Polymers91,7612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area2070 Å2
ΔGint-22 kcal/mol
Surface area31250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.165, 160.646, 162.021
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISTHRTHR(chain 'A' and (resid 2 through 18 or (resid 19...AA2 - 1068 - 112
12GLUGLUASPASP(chain 'A' and (resid 2 through 18 or (resid 19...AA118 - 126124 - 132
13ALAALAGLUGLU(chain 'A' and (resid 2 through 18 or (resid 19...AA128 - 131134 - 137
14ILEILEILEILE(chain 'A' and (resid 2 through 18 or (resid 19...AA134 - 397140 - 403
21HISHISTHRTHR(chain 'B' and (resid 2 through 99 or (resid 100...BB2 - 1068 - 112
22GLUGLUASPASP(chain 'B' and (resid 2 through 99 or (resid 100...BB118 - 126124 - 132
23ALAALAGLUGLU(chain 'B' and (resid 2 through 99 or (resid 100...BB128 - 131134 - 137
24ILEILEILEILE(chain 'B' and (resid 2 through 99 or (resid 100...BB134 - 397140 - 403
31HISHISTHRTHR(chain 'C' and (resid 2 through 18 or (resid 19...CC2 - 1068 - 112
32GLUGLUASPASP(chain 'C' and (resid 2 through 18 or (resid 19...CC118 - 126124 - 132
33ALAALAGLUGLU(chain 'C' and (resid 2 through 18 or (resid 19...CC128 - 131134 - 137
34ILEILEILEILE(chain 'C' and (resid 2 through 18 or (resid 19...CC134 - 397140 - 403

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Components

#1: Protein Saccharopine dehydrogenase


Mass: 45880.531 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: NCTC 11637 = CCUG 17874 = ATCC 43504 = JCM 12093 / Gene: NCTC11637_00022 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2X5A3P4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.6 Å3/Da / Density % sol: 65.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEC 3350, calcium acetate hydrate, Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 44580 / % possible obs: 99.9 % / Redundancy: 5.2 % / Biso Wilson estimate: 63.7 Å2 / CC1/2: 0.994 / Net I/σ(I): 20.5
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2205 / CC1/2: 0.746 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8H4Z

8h4z


Resolution: 2.9→29.9 Å / SU ML: 0.3582 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.9695
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2344 2277 5.16 %
Rwork0.1949 41836 -
obs0.1969 44113 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 77.51 Å2
Refinement stepCycle: LAST / Resolution: 2.9→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8966 0 0 4 8970
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00629156
X-RAY DIFFRACTIONf_angle_d0.919912452
X-RAY DIFFRACTIONf_chiral_restr0.0571418
X-RAY DIFFRACTIONf_plane_restr0.00591606
X-RAY DIFFRACTIONf_dihedral_angle_d24.26213228
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.960.38991470.32582573X-RAY DIFFRACTION99.49
2.96-3.030.35381460.3072568X-RAY DIFFRACTION99.41
3.03-3.110.36041460.29012577X-RAY DIFFRACTION99.74
3.11-3.190.31771280.26522609X-RAY DIFFRACTION99.85
3.19-3.290.30451410.26372578X-RAY DIFFRACTION99.85
3.29-3.390.29141380.23982606X-RAY DIFFRACTION99.85
3.39-3.510.25961520.21142591X-RAY DIFFRACTION99.85
3.51-3.650.23871370.20042604X-RAY DIFFRACTION99.82
3.65-3.820.21591360.17782616X-RAY DIFFRACTION99.89
3.82-4.020.22891480.17412591X-RAY DIFFRACTION99.78
4.02-4.270.18271390.1622625X-RAY DIFFRACTION99.71
4.27-4.60.17421650.14982592X-RAY DIFFRACTION99.89
4.6-5.060.1731400.14832644X-RAY DIFFRACTION99.96
5.06-5.790.2151420.16932632X-RAY DIFFRACTION99.93
5.79-7.270.24451410.19622673X-RAY DIFFRACTION99.96
7.27-29.90.23011310.18772757X-RAY DIFFRACTION99.01
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)
15.76647017381-1.931386481941.908524855122.85471953086-1.691170005626.195569673390.06528659600090.15187983240.3274406986280.0513745233149-0.0801841565475-0.0125224426714-0.5060407867360.176788864805-0.01018647638890.327012783894-0.01811141065540.02973933232250.3693415881130.004084804560930.3419308395568.27113448177-50.9700446042-2.32993618771
22.24960977322-0.690168737972-0.9370656063831.343523975020.9844180997622.169733533780.0394295331251-0.399539226051-0.115435313698-0.00742542174511-0.00558291391670.0265172787321-0.373708735377-0.600456032235-0.02295063521220.5516552551970.1529370799830.01719110415221.013826763650.1509676803950.667271620112-13.9723787982-39.26790321781.12643824589
34.22931657282-1.401153998081.251064320942.471885694510.1661628115824.172838207250.331501921660.730148936118-0.227315802842-0.394584556232-0.2137091734230.353264565746-0.247881075738-0.408621817863-0.1150719813220.4153125856660.108553947098-0.04412897949070.6452759570180.0209148388180.420678848851-3.77708533312-51.1952357121-13.5308113236
42.572375799092.7770223432-0.943670486562.99343348285-0.6258864069464.18374753531-0.133828829184-0.3183101635960.807190754387-0.238172239780.1583862128270.337217076276-0.986401145544-0.03047768292680.02539161682450.7756049232430.22115503117-0.1732069019250.734010658294-0.04188598219520.892654420091-30.3108481398-19.91249312146.9525949333
52.238608056380.9470451582260.5147788829913.713425779680.1971124142941.85572645206-0.204673285587-0.5175309344890.03192952376920.1046360680360.220207146147-0.272194257774-0.2048830638530.146843749302-0.05151720968560.5385845723130.264350468025-0.05720593786571.044371850370.03191270995250.628541315735-34.3800257722-35.036438109952.1100448106
61.303669591830.2950294065790.2122085540781.685776751740.07443686465563.774556264560.0008295097611640.2388383034280.378789481385-0.02099541780990.01150442190850.223591636189-0.38178832212-0.682914184609-0.003155951237030.6278717814490.3691688541910.007709852061691.202646166750.2258240426940.70412747917-46.9567603132-33.178397155131.7268201799
71.243502974830.5332327301-1.079281163860.632074971278-0.009215059271412.416344109630.1150214364690.1118401118770.0385790152093-0.0634176890393-0.0182873991904-0.0341878014801-0.09542125395610.00695816335882-0.1065513144190.5701782513030.228475643506-0.02638151077251.228094469050.1754546612230.583824496072-35.5754204664-40.756845184126.8665708882
83.442110714380.7672830221430.2832075696572.089325484470.7084382793312.23100787513-0.310915021853-0.1166849184850.8037067796170.04016217340850.07614633748170.423508606957-0.684964253404-1.123333238550.2138351352010.6575902454390.402461290638-0.03605223820761.18785227980.1001253253710.71797212515-48.7818062356-27.544894143639.0379898137
92.00981753003-0.255475642195-0.6557939753023.30062687889-0.962895409365.689620041440.012575143574-0.315287912823-0.02850427406360.2020731523920.0954708926474-0.0574500615565-0.1358990264350.458440014038-0.1037941794580.327689438408-0.0222368626172-0.05363056109550.578120147161-0.08342042717620.39255241921830.0161649715-60.273440691822.8117967266
101.560664987070.52465699485-0.9704312794790.603214188085-0.007070283912583.63261022935-0.0702858454187-0.101137936955-0.1492248036910.1364256883380.05295996137860.1647636616290.4687386350430.4455352508220.01965241851640.8097771255730.111393279762-0.07115462977460.4366492488980.02603014492250.51186685715615.6481280861-80.119714547826.0616119517
112.38949545605-1.630906031170.8454612646494.881764512241.534058968142.268177043-0.0901817989190.176902365253-0.4747901279040.02607706488110.255014635134-0.5289864382490.9433719123411.44655773424-0.197551125980.5975060667090.244140191745-0.02913424336210.776265713786-0.09455497632940.55240015590934.3664753138-75.54153467420.1078027291
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 160 )
2X-RAY DIFFRACTION2chain 'A' and (resid 161 through 302 )
3X-RAY DIFFRACTION3chain 'A' and (resid 303 through 398 )
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 50 )
5X-RAY DIFFRACTION5chain 'B' and (resid 51 through 145 )
6X-RAY DIFFRACTION6chain 'B' and (resid 146 through 184 )
7X-RAY DIFFRACTION7chain 'B' and (resid 185 through 304 )
8X-RAY DIFFRACTION8chain 'B' and (resid 305 through 399 )
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 145 )
10X-RAY DIFFRACTION10chain 'C' and (resid 146 through 338 )
11X-RAY DIFFRACTION11chain 'C' and (resid 339 through 399 )

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