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- PDB-8h52: Crystal structure of Helicobacter pylori carboxyspermidine dehydr... -

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Basic information

Entry
Database: PDB / ID: 8h52
TitleCrystal structure of Helicobacter pylori carboxyspermidine dehydrogenase in complex with NADP
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 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Saccharopine dehydrogenase
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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 / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / 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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6242
Polymers45,8811
Non-polymers7431
Water00
1
A: Saccharopine dehydrogenase
hetero molecules

A: Saccharopine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,2484
Polymers91,7612
Non-polymers1,4872
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_455-x-1/2,y,-z1
Buried area4820 Å2
ΔGint-26 kcal/mol
Surface area29230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)194.077, 194.077, 194.077
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
Space group name HallI2b2c3
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z+1/2,x
#5: z,-x,-y+1/2
#6: -y+1/2,z,-x
#7: -z,-x+1/2,y
#8: -z+1/2,x,-y
#9: y,-z,-x+1/2
#10: x,-y,-z+1/2
#11: -x+1/2,y,-z
#12: -x,-y+1/2,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1,x+1/2
#17: z+1/2,-x+1/2,-y+1
#18: -y+1,z+1/2,-x+1/2
#19: -z+1/2,-x+1,y+1/2
#20: -z+1,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1
#22: x+1/2,-y+1/2,-z+1
#23: -x+1,y+1/2,-z+1/2
#24: -x+1/2,-y+1,z+1/2

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Components

#1: Protein Saccharopine dehydrogenase


Mass: 45880.531 Da / Num. of mol.: 1
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: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
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: 6.64 Å3/Da / Density % sol: 81.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: ammonium sulfate, NaCl, Bis-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: Mar 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.1→30 Å / Num. obs: 22284 / % possible obs: 100 % / Redundancy: 15.1 % / Biso Wilson estimate: 81.47 Å2 / CC1/2: 0.993 / Net I/σ(I): 18.1
Reflection shellResolution: 3.1→3.15 Å / Redundancy: 14.3 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1118 / CC1/2: 0.325 / % 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: 3.1→29.95 Å / SU ML: 0.4263 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.8229
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2505 1082 4.92 %
Rwork0.2019 20927 -
obs0.2041 22009 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 88.1 Å2
Refinement stepCycle: LAST / Resolution: 3.1→29.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3084 0 0 0 3084
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01033155
X-RAY DIFFRACTIONf_angle_d1.06784304
X-RAY DIFFRACTIONf_chiral_restr0.0545484
X-RAY DIFFRACTIONf_plane_restr0.0064555
X-RAY DIFFRACTIONf_dihedral_angle_d20.01431843
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.240.33511420.31742614X-RAY DIFFRACTION99.93
3.24-3.410.34461570.27192571X-RAY DIFFRACTION99.82
3.41-3.630.29841400.24432607X-RAY DIFFRACTION99.75
3.63-3.90.30031340.21432578X-RAY DIFFRACTION98.76
3.9-4.30.26041510.20992556X-RAY DIFFRACTION97.73
4.3-4.920.21121130.1692604X-RAY DIFFRACTION98.73
4.92-6.190.21441400.18662647X-RAY DIFFRACTION99.64
6.19-29.950.2031050.17152750X-RAY DIFFRACTION99.79
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)
10.6007647559670.239298591573-0.2201909582851.62037829084-0.7663681964430.9438655638510.5610673980650.0256253384880.656957910567-0.07207236855630.2751996360080.202282955063-0.77265909777-0.1700591530920.03897711544681.38904305829-0.2895770545741.224351403810.0812676880740.3039592777251.33048835552-26.53305570985.73645665565-24.0662702537
20.760550561720.349842950678-0.61048148691.46117404798-1.366718421581.36810580660.623000686199-0.5655822616280.6739975414290.2936290720040.331538412277-0.38193852717-0.6321954933080.450401648482-0.3307690321011.38654001665-0.1137650145950.6724118476390.606092816028-0.1700249429691.53042640547-23.53119227629.3738778212-19.5686187376
3-3.68812063001E-50.0466909433840.002065308125470.7373962594920.1532438295990.01251495535840.1495293282670.05068293107531.43300547863-0.3100153615380.211984096652-0.432217471935-1.31678651597-0.0452659066142-0.08346665962031.76336164609-0.01111293137341.029545256550.2156742596740.4009169813521.91412543976-32.068599302715.509012112-24.85453581
41.70948944105-1.373391588791.09345206673.11788731722-0.5654372431120.7067195884810.4507768685220.1065829135911.29428118731-0.354145282405-0.3332010971380.547464336755-1.4052933259-1.29956117509-0.4839116261321.475720299720.7126515783710.6475412625550.6655382645430.7689054812931.35988722632-43.84893170946.8040087982-30.4636788788
51.5864203106-0.150889469643-1.065216457661.01861226981-0.5683522552211.855440442160.2345832288010.3193774455360.2208005447970.007808516256440.01736707998120.22808351926-0.361247291969-0.309695498693-0.1380791389790.5991006379750.1555503394170.1642688719710.7248286282880.2051042421120.585120093723-38.3684805755-13.1077325844-26.4451328825
62.18415477606-0.21602352859-1.020322760221.81618416583-0.05485532960212.059515893220.1208360419440.8938057696460.3453413338850.1225905049620.003386921416710.697313366458-0.530619266049-0.886474053476-0.1577199601640.6258506535060.1866688378590.2579467678760.9022454451010.2148292978070.852144762046-48.1620017159-14.1961983857-20.8081281212
71.98655006636-0.39738640263-0.8762443057571.688039541970.251151266684.393194118730.345158750570.6585988905410.1707070056270.184526568137-0.159090150010.274273553355-0.130114172313-1.17742633936-0.194436664880.6344526086980.2066948046510.211642078120.8252559689830.1985898468860.750417283338-47.7798185314-11.8355331177-20.6249034826
80.423307067882-0.314694421142-0.1168102650050.2994535613190.1530109400580.1106918284210.578559754451-0.3057936290980.8822788293990.840116739210.3791384219690.526100828263-1.26389098733-0.252105374686-0.2997745086951.443740488680.09236701523270.7026757167790.5486968548340.01361717003691.28305688943-50.24805583686.29436000886-4.11755919999
92.838007913630.164170076148-1.115588794682.00620026166-0.4576854521411.935583118920.3567475245520.02556726452530.5613234260780.06133006873490.07115050321160.111438256398-0.581744313170.180257866916-0.3478531420390.5659212515830.04638556801180.2057831488170.5173047369070.1254748850410.559378997321-31.4446963519-10.8152785109-24.1860331251
101.99000676384-0.7517253138280.9271125356212.73537762097-1.525780732152.038588711940.3943544170610.7694672796890.463527389882-0.666719237819-0.120935623822-0.0932572256531-0.734463325239-0.262376721775-0.1993881029580.8915858465440.2577320781610.2993892187580.7587724779850.2525287592330.737445439803-31.6154746755-5.73051504971-37.6528830311
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 22 )
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 50 )
3X-RAY DIFFRACTION3chain 'A' and (resid 51 through 85 )
4X-RAY DIFFRACTION4chain 'A' and (resid 86 through 145 )
5X-RAY DIFFRACTION5chain 'A' and (resid 146 through 184 )
6X-RAY DIFFRACTION6chain 'A' and (resid 185 through 231 )
7X-RAY DIFFRACTION7chain 'A' and (resid 232 through 267 )
8X-RAY DIFFRACTION8chain 'A' and (resid 268 through 291 )
9X-RAY DIFFRACTION9chain 'A' and (resid 292 through 359 )
10X-RAY DIFFRACTION10chain 'A' and (resid 360 through 399 )

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