[English] 日本語
Yorodumi
- PDB-8h52: Crystal structure of Helicobacter pylori carboxyspermidine dehydr... -

+
Open data


ID or keywords:

Loading...

-
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 / homology
Function and homology information


Saccharopine dehydrogenase, NADP binding domain / Saccharopine dehydrogenase-like, C-terminal / Saccharopine dehydrogenase NADP binding domain / Saccharopine dehydrogenase C-terminal domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Saccharopine dehydrogenase
Similarity search - Component
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more