[English] 日本語
Yorodumi
- PDB-9bpl: Crystal structure of Adenylosuccinate Lyase from Leishmania major -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9bpl
TitleCrystal structure of Adenylosuccinate Lyase from Leishmania major
ComponentsAdenylosuccinate lyase
KeywordsLYASE / Adenylossucinate lyase / ASL / Leishmania major
Function / homology
Function and homology information


adenylosuccinate lyase / N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity / (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido) succinate lyase (fumarate-forming) activity / 'de novo' AMP biosynthetic process / 'de novo' IMP biosynthetic process / nucleoplasm / cytoplasm
Similarity search - Function
Adenylosuccinate lyase PurB, C-terminal / : / Adenylosuccinate lyase C-terminal / Adenylosuccinate lyase / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Fumarase/histidase, N-terminal / L-Aspartase-like
Similarity search - Domain/homology
PHOSPHATE ION / Adenylosuccinate lyase
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsRosa e Silva, I. / Mantovani, M. / Nagem, R. / Cardona, A. / Reboredo, E. / Thiemann, O.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)01/10216-3 Brazil
CitationJournal: To Be Published
Title: Crystal Structure of Adenylosuccinate lyase from Leishmania major
Authors: Rosa e Silva, I. / Mantovani, M. / Nagem, R. / Cardona, A. / Reboredo, E. / Thiemann, O.
History
DepositionMay 7, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Adenylosuccinate lyase
B: Adenylosuccinate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,42214
Polymers107,5512
Non-polymers87112
Water7,476415
1
A: Adenylosuccinate lyase
B: Adenylosuccinate lyase
hetero molecules

A: Adenylosuccinate lyase
B: Adenylosuccinate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,84328
Polymers215,1014
Non-polymers1,74224
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_655-x+1,-y,z1
Buried area35530 Å2
ΔGint-336 kcal/mol
Surface area58170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.020, 130.020, 316.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 14 through 22 or resid 25...
d_2ens_1(chain "B" and (resid 14 through 73 or (resid 74...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11VALVALPROPROAA14 - 2214 - 22
d_12ILEILETHRTHRAA25 - 11625 - 116
d_13ASPASPPHEPHEAA119 - 209119 - 209
d_14VALVALTHRTHRAA211 - 221211 - 221
d_15LEULEULEULEUAA223 - 294223 - 294
d_16ASPASPLYSLYSAA296 - 313296 - 313
d_17HISHISGLUGLUAA326 - 334326 - 334
d_18ALAALALEULEUAA336 - 419336 - 419
d_19ARGARGLEULEUAA421 - 434421 - 434
d_110HISHISPROPROAA440 - 479440 - 479
d_111GOLGOLGOLGOLAC501
d_21VALVALARGARGBB14 - 9414 - 94
d_22THRTHRGLYGLYBB96 - 13596 - 135
d_23GLUGLUALAALABB137 - 138137 - 138
d_24LYSLYSPHEPHEBB140 - 209140 - 209
d_25VALVALTHRTHRBB211 - 221211 - 221
d_26LEULEULEULEUBB223 - 294223 - 294
d_27ASPASPGLUGLUBB296 - 334296 - 334
d_28ALAALALEULEUBB336 - 419336 - 419
d_29ARGARGLEULEUBB421 - 434421 - 434
d_210HISHISPROPROBB440 - 479440 - 479
d_211GOLGOLGOLGOLBK502

NCS oper: (Code: givenMatrix: (-0.687717846028, 0.725940260116, -0.0074096556277), (0.725945061539, 0.687748087256, 0.00251716161285), (0.00692328544116, -0.00364790594814, -0.999969379982)Vector: ...NCS oper: (Code: given
Matrix: (-0.687717846028, 0.725940260116, -0.0074096556277), (0.725945061539, 0.687748087256, 0.00251716161285), (0.00692328544116, -0.00364790594814, -0.999969379982)
Vector: 109.656367735, -47.3684690886, -32.2711960983)

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Adenylosuccinate lyase / ASL / Adenylosuccinase


Mass: 53775.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: LMJF_04_0460 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9U0T7, adenylosuccinate lyase

-
Non-polymers , 6 types, 427 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.14 Å3/Da / Density % sol: 60.86 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion
Details: 3 uL of protein solution at 10 mg.mL-1 (in a buffer containing 5 mM KPO4, 5 mM NaCl, 100 uM ADS) and 3 uL of reservoir solution (1.6 M ammonium sulfate, 0.1 M MES pH 6.5, 10% dioxane)

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.542 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 25, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.97→25.25 Å / Num. obs: 95392 / % possible obs: 99.8 % / Redundancy: 14.2 % / Biso Wilson estimate: 30.88 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.028 / Rrim(I) all: 0.108 / Net I/σ(I): 18.7
Reflection shellResolution: 1.97→2 Å / Rmerge(I) obs: 1.373 / Num. unique obs: 4603 / CC1/2: 0.792 / Rpim(I) all: 0.382 / % possible all: 99.2

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
iMOSFLMdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→25.25 Å / SU ML: 0.2355 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.9307
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2394 4714 4.96 %
Rwork0.2108 90295 -
obs0.2122 95009 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.56 Å2
Refinement stepCycle: LAST / Resolution: 1.97→25.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7027 0 48 415 7490
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087280
X-RAY DIFFRACTIONf_angle_d0.98329880
X-RAY DIFFRACTIONf_chiral_restr0.05411124
X-RAY DIFFRACTIONf_plane_restr0.0091257
X-RAY DIFFRACTIONf_dihedral_angle_d15.1148982
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.76085265451 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-1.990.35081650.29542934X-RAY DIFFRACTION99.07
1.99-2.020.28741510.27992967X-RAY DIFFRACTION99.17
2.02-2.040.27951820.27292943X-RAY DIFFRACTION99.24
2.04-2.070.28951430.26652996X-RAY DIFFRACTION99.34
2.07-2.090.33071770.24742939X-RAY DIFFRACTION99.3
2.09-2.120.23561510.24432973X-RAY DIFFRACTION99.46
2.12-2.150.25031680.23362979X-RAY DIFFRACTION99.46
2.15-2.180.31371510.2492989X-RAY DIFFRACTION99.46
2.18-2.220.27921750.24562963X-RAY DIFFRACTION99.56
2.22-2.250.3481530.31192948X-RAY DIFFRACTION98.63
2.25-2.290.32171380.26822974X-RAY DIFFRACTION98.7
2.29-2.340.29371690.23052967X-RAY DIFFRACTION99.71
2.34-2.380.31851560.24213018X-RAY DIFFRACTION99.78
2.38-2.430.30051890.23832968X-RAY DIFFRACTION99.75
2.43-2.480.26321340.22093011X-RAY DIFFRACTION99.75
2.48-2.540.22371400.21163020X-RAY DIFFRACTION99.53
2.54-2.60.24551560.21822995X-RAY DIFFRACTION99.75
2.6-2.670.27591460.21963016X-RAY DIFFRACTION99.56
2.67-2.750.27981590.22912994X-RAY DIFFRACTION99.56
2.75-2.840.22671580.22873004X-RAY DIFFRACTION99.22
2.84-2.940.25921620.22982991X-RAY DIFFRACTION98.9
2.94-3.060.2591570.22883026X-RAY DIFFRACTION99.34
3.06-3.20.25251470.23013012X-RAY DIFFRACTION99.31
3.2-3.370.24671420.21693050X-RAY DIFFRACTION99.53
3.37-3.580.20531440.20213044X-RAY DIFFRACTION99.35
3.58-3.850.20341560.17693039X-RAY DIFFRACTION99.44
3.85-4.240.18651540.16683061X-RAY DIFFRACTION99.08
4.24-4.850.21460.16713086X-RAY DIFFRACTION99.26
4.85-6.090.22541600.19223131X-RAY DIFFRACTION99.79
6.09-25.250.19251850.18483257X-RAY DIFFRACTION99.65
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)
11.409924466481.07308371682-1.264475768870.770248304115-0.6951313631881.757640444050.0484961346159-0.2966502269440.1069888637780.032417469037-0.2731375052070.291366696368-0.259124194769-1.156515737380.0847793302320.134064288698-0.2111359149430.05758743163931.239494190620.003866508241890.42193351795334.31223050090.539196130623-5.09990863845
20.5465637594510.137117902509-0.09457439055910.50822174697-0.09212702931111.23884218089-0.02617538724150.0116919122308-0.0682912065314-0.0346561242018-0.01635887818950.1461155570180.442520215193-0.7503347017990.03516081098840.244403321193-0.1764897277450.006056391308970.430496449641-0.02371813054770.30716670559349.346755819-9.44111443858-18.3090419971
35.45462984271-4.238366628610.05334486063045.777223084091.781036901553.95546127620.151518419780.320127326263-0.00105420624641-0.414344438512-0.0511672013395-0.3697832016630.4629396567530.272577965784-0.1041984548440.524846486373-0.0828527590150.05943100625070.321672717795-0.0322215010890.26937194586671.7624491952-21.5999174655-57.5920478983
41.263751861610.6773258195670.4578098422861.633127739910.9482649220672.26412649635-0.06067566061220.0580572951292-0.302725876286-0.2244100227410.196031561709-0.4452929316840.6581534011820.974226652391-0.1677527179560.539211947680.2384733177910.0618101068040.5711431574020.006250906339950.38648326554986.118663408-22.9326124701-26.8557028253
50.455735533313-0.0221934842338-0.1530402862930.6986279837710.2328641781892.76754175125-0.0741192115938-0.0603865769453-0.152576979417-0.0228726795478-0.0095487883058-0.01134838716690.7768176425030.09617577156970.07400725203380.30902598116-0.006908002607310.03880788665090.1847416624360.01713945278840.26075121219869.0580611273-18.1212753155-14.0742880709
69.23988582378-0.585478102069-3.913782047320.9022649409460.2488567603513.10033800759-0.132528429786-0.293705719812-0.05058036768320.1665010697480.05932472513480.2130671838740.302483005953-0.3792080937270.0634691754180.360650144902-0.09718869641920.07860610279320.5305959760380.04722944251210.26391137330145.2977579402-10.581717978125.7589039507
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 14 through 129 )AA14 - 1291 - 114
22chain 'A' and (resid 130 through 395 )AA130 - 395115 - 365
33chain 'A' and (resid 396 through 479 )AA396 - 479366 - 445
44chain 'B' and (resid 14 through 129 )BK14 - 1291 - 112
55chain 'B' and (resid 130 through 395 )BK130 - 395113 - 364
66chain 'B' and (resid 396 through 479 )BK396 - 479365 - 444

+
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