[English] 日本語
Yorodumi
- PDB-5us8: 2.15 Angstrom Resolution Crystal Structure of Argininosuccinate S... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5us8
Title2.15 Angstrom Resolution Crystal Structure of Argininosuccinate Synthase from Bordetella pertussis
ComponentsArgininosuccinate synthase
KeywordsHYDROLASE / OXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Argininosuccinate Synthase
Function / homology
Function and homology information


argininosuccinate synthase / argininosuccinate synthase activity / arginine biosynthetic process / protein homodimerization activity / ATP binding / cytoplasm
Similarity search - Function
Helix Hairpins - #400 / Argininosuccinate synthase, type 2 subfamily / Argininosuccinate synthetase mutimerisation domain, C-terminal tail / Argininosuccinate synthetase, chain A, domain 2 / Argininosuccinate synthetase, chain A, domain 2 / Argininosuccinate synthase / Argininosuccinate synthase, conserved site / Argininosuccinate synthetase, catalytic/multimerisation domain body / Arginosuccinate synthase N-terminal HUP domain / Argininosuccinate synthase signature 1. ...Helix Hairpins - #400 / Argininosuccinate synthase, type 2 subfamily / Argininosuccinate synthetase mutimerisation domain, C-terminal tail / Argininosuccinate synthetase, chain A, domain 2 / Argininosuccinate synthetase, chain A, domain 2 / Argininosuccinate synthase / Argininosuccinate synthase, conserved site / Argininosuccinate synthetase, catalytic/multimerisation domain body / Arginosuccinate synthase N-terminal HUP domain / Argininosuccinate synthase signature 1. / Argininosuccinate synthase signature 2. / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Helix Hairpins / Alpha-Beta Complex / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE / TRIETHYLENE GLYCOL / Argininosuccinate synthase
Similarity search - Component
Biological speciesBordetella pertussis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsMinasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Stam, J. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 2.15 Angstrom Resolution Crystal Structure of Argininosuccinate Synthase from Bordetella pertussis
Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Stam, J. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionFeb 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Argininosuccinate synthase
B: Argininosuccinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,5238
Polymers99,2942
Non-polymers1,2286
Water9,404522
1
A: Argininosuccinate synthase
B: Argininosuccinate synthase
hetero molecules

A: Argininosuccinate synthase
B: Argininosuccinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,04516
Polymers198,5894
Non-polymers2,45712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x,-y,z1
Buried area33660 Å2
ΔGint-77 kcal/mol
Surface area66270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.453, 94.453, 188.490
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Components on special symmetry positions
IDModelComponents
11A-785-

HOH

21B-769-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: -2 - 442 / Label seq-ID: 1 - 445

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

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Argininosuccinate synthase / Citrulline--aspartate ligase


Mass: 49647.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251) (bacteria)
Strain: Tohama I / ATCC BAA-589 / NCTC 13251 / Gene: argG, BP3537 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-Magic / References: UniProt: Q7VTJ9, argininosuccinate synthase

-
Non-polymers , 5 types, 528 molecules

#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 522 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein: 10.6 mg/ml, 0.01M Tris HCl (pH 8.3), ATP, Mg; Screen: Classics II (G8), 0.2M Ammonium acetate, 0.1 HEPES (pH 7.5), 25% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 2, 2017 / Details: C(111)
RadiationMonochromator: beryllium lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. obs: 51703 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 44.4 Å2 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.031 / Rsym value: 0.077 / Χ2: 1.012 / Net I/σ(I): 23.3
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.759 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2558 / CC1/2: 0.79 / Rpim(I) all: 0.298 / Rsym value: 0.759 / Χ2: 1.014 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K92

1k92


Resolution: 2.15→29.46 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.958 / SU B: 8.882 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.218 / ESU R Free: 0.173 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20032 2519 4.9 %RANDOM
Rwork0.15605 ---
obs0.15812 49016 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 52.267 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0.04 Å20 Å2
2---0.08 Å20 Å2
3---0.27 Å2
Refinement stepCycle: 1 / Resolution: 2.15→29.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6934 0 79 522 7535
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0197222
X-RAY DIFFRACTIONr_bond_other_d0.0010.026711
X-RAY DIFFRACTIONr_angle_refined_deg1.3811.9779794
X-RAY DIFFRACTIONr_angle_other_deg0.893315540
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.8545904
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.16223.935338
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.281151215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.781560
X-RAY DIFFRACTIONr_chiral_restr0.0850.21076
X-RAY DIFFRACTIONr_gen_planes_refined0.0230.0218113
X-RAY DIFFRACTIONr_gen_planes_other0.0190.021486
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9133.6783598
X-RAY DIFFRACTIONr_mcbond_other1.9123.6773597
X-RAY DIFFRACTIONr_mcangle_it2.9595.5054508
X-RAY DIFFRACTIONr_mcangle_other2.965.5074509
X-RAY DIFFRACTIONr_scbond_it2.284.023623
X-RAY DIFFRACTIONr_scbond_other2.284.023623
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5125.915287
X-RAY DIFFRACTIONr_long_range_B_refined6.28344.4798224
X-RAY DIFFRACTIONr_long_range_B_other6.21943.888089
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 28252 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 195 -
Rwork0.22 3570 -
obs--99.97 %
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)
11.5060.49470.8660.57450.22270.82020.01280.0451-0.0720.03760.03420.10540.1292-0.0429-0.04690.1673-0.0714-0.01890.03640.00880.0953-24.6226-19.7361-17.6257
22.64531.23780.65952.28571.13791.44050.0807-0.1862-0.01810.2953-0.15590.3360.2818-0.19050.07520.1838-0.06940.00760.04490.02190.1347-33.0153-18.0951-11.9369
31.1180.24860.04421.55390.30211.50730.09510.023-0.31690.0133-0.06880.13790.2965-0.329-0.02630.2815-0.0959-0.05160.0890.01450.2706-13.2239-33.5661-2.5777
41.29450.0845-0.11280.83680.11111.74990.1030.2364-0.3082-0.11980.0395-0.00970.1258-0.0085-0.14250.2255-0.0293-0.0510.055-0.05520.1285-0.518-26.4923-15.8643
50.76720.04010.01920.6977-0.1080.48850.05770.0681-0.1173-0.0258-0.0043-0.07120.03150.0516-0.05340.1674-0.044-0.0220.0348-0.02380.05424.2878-14.6317-9.6952
62.66790.5452-1.45730.7071-0.84991.45350.1543-0.36990.02560.0777-0.10310.0282-0.26860.1667-0.05120.209-0.0493-0.02540.2336-0.02490.099519.63731.794517.5703
71.2461-0.17090.81880.2455-0.02390.73130.0582-0.0286-0.1145-0.02840.0424-0.10950.15480.0866-0.10060.1987-0.0061-0.04130.1650.00260.165228.521-13.949517.5036
81.6854-0.48130.94451.1819-0.83081.79490.10010.126-0.0228-0.2489-0.1305-0.23040.29640.49230.03030.13760.0442-0.0060.17490.00060.11736.2026-11.948411.3651
91.1291-0.06150.03770.9129-0.19460.77670.1047-0.1712-0.29540.1348-0.0364-0.10810.10930.0847-0.06830.1915-0.044-0.0770.05150.03490.129810.2806-24.56368.5957
100.94730.0374-0.06440.85870.09750.47190.062-0.1368-0.08450.11370.00630.0960.0694-0.048-0.06830.1743-0.0643-0.0250.07040.04040.0461-3.3733-14.334111.099
113.34970.2358-1.81391.9978-0.50462.22270.16570.26220.4363-0.140.1930.3389-0.2235-0.2069-0.35860.2264-0.0458-0.03330.16040.01040.1536-21.8453-1.2481-12.7243
122.47040.58911.10960.14190.2640.59130.1044-0.4020.23630.0322-0.10760.0576-0.0597-0.2230.00320.24580.01430.10150.1945-0.00780.1449-10.2796-7.8715-37.0814
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 119
2X-RAY DIFFRACTION2A120 - 184
3X-RAY DIFFRACTION3A185 - 233
4X-RAY DIFFRACTION4A234 - 282
5X-RAY DIFFRACTION5A283 - 394
6X-RAY DIFFRACTION6A395 - 442
7X-RAY DIFFRACTION7B-2 - 119
8X-RAY DIFFRACTION8B120 - 189
9X-RAY DIFFRACTION9B190 - 317
10X-RAY DIFFRACTION10B318 - 394
11X-RAY DIFFRACTION11B395 - 431
12X-RAY DIFFRACTION12B432 - 442

+
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://pdbjlvh1.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