[English] 日本語
Yorodumi
- PDB-5g2h: S. enterica HisA with mutation L169R -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5g2h
TitleS. enterica HisA with mutation L169R
Components1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase
KeywordsISOMERASE / HISA / PROTEIN EVOLUTION / IAD MODEL / TRPF
Function / homology
Function and homology information


1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase / 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase activity / L-histidine biosynthetic process / L-tryptophan biosynthetic process / cytoplasm
Similarity search - Function
HisA, bacterial-type / HisA/PriA, bacterial-type / Histidine biosynthesis, HisA-like / Histidine biosynthesis protein / Histidine biosynthesis protein / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase / 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase
Similarity search - Component
Biological speciesSalmonella enterica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsNewton, M. / Guo, X. / Soderholm, A. / Nasvall, J. / Duarte, F. / Andersson, D. / Patrick, W. / Selmer, M.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structural and functional innovations in the real-time evolution of new ( beta alpha )8 barrel enzymes.
Authors: Newton, M.S. / Guo, X. / Soderholm, A. / Nasvall, J. / Lundstrom, P. / Andersson, D.I. / Selmer, M. / Patrick, W.M.
History
DepositionApr 8, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2017Group: Database references
Revision 1.2May 10, 2017Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / entity_name_com / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_mod_residue / pdbx_struct_special_symmetry / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity_name_com.name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_mod_residue.details / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9369
Polymers27,2521
Non-polymers6848
Water2,180121
1
A: 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase
hetero molecules

A: 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,87118
Polymers54,5042
Non-polymers1,36716
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/31
Buried area3560 Å2
ΔGint-147.9 kcal/mol
Surface area20110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.017, 86.017, 122.688
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-1252-

SO4

21A-1252-

SO4

31A-2103-

HOH

-
Components

#1: Protein 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase / Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase


Mass: 27252.080 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica (bacteria) / Gene: hisA, B5647_05330 / Plasmid: PEXP5-CT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0A5U0GD61, UniProt: P10372*PLUS, 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growpH: 7 / Details: 0.1 M NA ACETATE PH 4.6, 2.3 M AMMONIUM SULFATE

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 40024 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.8 % / Biso Wilson estimate: 21.04 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 9.15
Reflection shellResolution: 1.9→2 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.3 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5AHE

5ahe


Resolution: 1.9→47.354 Å / SU ML: 0.2 / σ(F): 1.37 / Phase error: 18.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2119 1982 4.9 %
Rwork0.1686 --
obs0.1708 40017 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.8 Å2
Refinement stepCycle: LAST / Resolution: 1.9→47.354 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1748 0 39 121 1908
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011894
X-RAY DIFFRACTIONf_angle_d1.1922586
X-RAY DIFFRACTIONf_dihedral_angle_d12.707701
X-RAY DIFFRACTIONf_chiral_restr0.045308
X-RAY DIFFRACTIONf_plane_restr0.005330
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-1.94760.28981420.24392719X-RAY DIFFRACTION100
1.9476-2.00020.27811420.22122721X-RAY DIFFRACTION100
2.0002-2.05910.25811430.19632688X-RAY DIFFRACTION100
2.0591-2.12560.21791420.18992710X-RAY DIFFRACTION100
2.1256-2.20150.22551390.18332741X-RAY DIFFRACTION100
2.2015-2.28970.2271390.17392699X-RAY DIFFRACTION100
2.2897-2.39390.16761400.16672740X-RAY DIFFRACTION100
2.3939-2.52010.21631430.16562708X-RAY DIFFRACTION100
2.5201-2.67790.25451400.16852734X-RAY DIFFRACTION100
2.6779-2.88470.19931400.16442711X-RAY DIFFRACTION100
2.8847-3.17490.17321420.15372708X-RAY DIFFRACTION100
3.1749-3.63420.20261440.15312725X-RAY DIFFRACTION100
3.6342-4.57810.19351410.14232714X-RAY DIFFRACTION100
4.5781-47.36890.21531450.17872717X-RAY DIFFRACTION100
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)
10.37610.1097-0.11710.21250.18730.3507-0.13120.11210.03040.0520.0390.2176-0.1018-0.0366-0.08510.09460.0056-0.01110.10310.02210.16316.683331.9799-8.5731
21.10980.58380.38320.32260.18030.1615-0.1845-0.14770.6694-0.02350.06970.1934-0.2669-0.1565-0.02390.2535-0.0015-0.03530.1983-0.02650.26119.247436.8391-11.8709
30.09110.26230.03390.7464-0.07550.5456-0.0166-0.0721-0.1394-0.0303-0.0040.1756-0.10160.0343-0.0280.1320.00630.00470.1108-0.00510.18439.606127.2272-8.889
40.0599-0.1047-0.06970.412-0.16890.3718-0.3360.03460.13180.07550.51760.57670.2284-0.12880.00680.20470.0296-0.01660.2580.05450.4158-7.006127.4329-11.0115
50.16830.0498-0.04890.4510.26580.16650.00730.0013-0.0536-0.14310.08250.1032-0.06220.02810.03130.1294-0.0096-0.01710.12330.01450.12246.357923.3182-14.1218
60.20230.0189-0.07680.2108-0.30110.4233-0.13020.2818-0.1521-0.0717-0.05620.0910.072-0.4771-0.02070.1378-0.00150.00910.2063-0.0280.1505-2.752816.5455-10.2444
70.0587-0.05420.00850.0471-0.05740.0692-0.0903-0.0184-0.08030.04390.1225-0.0898-0.00060.10130.03090.12310.01130.02090.1184-0.0130.1174-1.174218.66270.1891
80.1247-0.0576-0.01650.01580.00190.102-0.23760.0408-0.3816-0.06490.13020.14320.3212-0.1625-0.00010.1859-0.010.04210.1505-0.00170.2004-2.23749.435-0.5619
90.15130.1131-0.04280.0879-0.05090.0395-0.1139-0.1432-0.09390.1380.1161-0.08840.17640.0475-0.00070.1593-0.02150.03360.1334-0.01220.14424.643116.47680.0405
100.1134-0.00510.10670.2358-0.06910.1479-0.1339-0.0362-0.00480.40770.07160.10220.08970.023-0.06180.19190.05520.00950.1794-0.00740.0992.251526.881217.7889
110.0865-0.0721-0.01970.0694-0.03660.07930.01140.26240.3171-0.12160.20640.28490.0315-0.00850.00080.18120.00780.00260.17040.04610.1901-5.570330.05789.6132
120.0328-0.0486-0.02570.05140.03330.0182-0.1972-0.2368-0.18520.130.19630.16280.10340.13080.00020.16620.02020.03540.15060.03520.17411.071316.743113.9516
130.2911-0.00040.10330.0539-0.03290.29890.0142-0.1085-0.03880.00390.0117-0.1596-0.08750.11120.00750.13730.00350.03880.0839-0.00010.14466.049118.07485.7168
140.01370.00490.00820.0271-0.06690.18210.4769-0.20270.20330.1481-0.0008-0.0987-0.4297-0.58620.00150.5451-0.07040.15630.3464-0.01220.500812.797133.96811.6968
150.02950.0081-0.02290.01940.00440.02540.10980.08280.34980.076-0.21870.1403-0.00110.221900.249-0.03370.0290.347-0.02260.254514.136224.349114.8863
160.8254-0.08510.190.10610.03751.02820.0986-0.164-0.06170.05710.0098-0.0341-0.13390.18190.50790.1390.00760.01710.15190.01980.104612.246718.86588.8244
170.7266-0.2311-0.4620.07420.14730.30260.6154-0.82320.5170.1504-0.292-0.19380.01880.12220.02370.2944-0.10980.01380.2894-0.02990.195320.126134.84974.9704
180.0360.0127-0.07540.0621-0.04430.27950.0914-0.1164-0.04740.033-0.1471-0.1571-0.07590.1562-0.0180.1481-0.0369-0.00330.17380.04280.18817.977727.74663.7857
190.0714-0.07030.07690.0948-0.05430.07570.0992-0.031-0.01930.0907-0.1181-0.1121-0.040.00550.05130.1513-0.04980.01640.11950.00030.123221.144235.2691-4.6727
200.51830.066-0.01450.17950.03730.01420.1784-0.7478-0.28590.2447-0.08910.1914-0.23390.31330.00350.2436-0.0374-0.03330.21230.03010.181426.219527.45731.7373
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:14)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 15:38)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 39:53)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 54:62)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 63:82)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 83:96)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 97:108)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 109:121)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 122:128)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 129:140)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 141:148)
12X-RAY DIFFRACTION12(CHAIN A AND RESID 149:159)
13X-RAY DIFFRACTION13(CHAIN A AND RESID 160:173)
14X-RAY DIFFRACTION14(CHAIN A AND RESID 174:184)
15X-RAY DIFFRACTION15(CHAIN A AND RESID 185:189)
16X-RAY DIFFRACTION16(CHAIN A AND RESID 190:204)
17X-RAY DIFFRACTION17(CHAIN A AND RESID 205:213)
18X-RAY DIFFRACTION18(CHAIN A AND RESID 214:228)
19X-RAY DIFFRACTION19(CHAIN A AND RESID 229:240)
20X-RAY DIFFRACTION20(CHAIN A AND RESID 241:244)

+
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