[English] 日本語
Yorodumi
- PDB-7su4: Dihydroneopterin aldolase (DHNA) Tyr53Phe from Yersinia pestis co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7su4
TitleDihydroneopterin aldolase (DHNA) Tyr53Phe from Yersinia pestis co-crystallized with 7,8-dihydroneopterin
Components7,8-dihydroneopterin aldolase
KeywordsBIOSYNTHETIC PROTEIN / FOLB FOLATE PATHWAY
Function / homology
Function and homology information


dihydroneopterin aldolase / dihydroneopterin aldolase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / kinase activity
Similarity search - Function
Dihydroneopterin aldolase / Dihydroneopterin aldolase/epimerase domain / Dihydroneopterin aldolase / Dihydroneopterin aldolase / GTP cyclohydrolase I, C-terminal/NADPH-dependent 7-cyano-7-deazaguanine reductase
Similarity search - Domain/homology
Chem-NPR / 7,8-dihydroneopterin aldolase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsBourne, C.R.
Funding support1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM103447
CitationJournal: To Be Published
Title: Dihydroneopterin aldolase (DHNA) Tyr53Phe from Yersinia pestis co-crystallized with 7,8-dihydroneopterin
Authors: Bourne, C.R. / Tan, A.
History
DepositionNov 16, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 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: 7,8-dihydroneopterin aldolase
B: 7,8-dihydroneopterin aldolase
C: 7,8-dihydroneopterin aldolase
D: 7,8-dihydroneopterin aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,16614
Polymers64,5334
Non-polymers1,63410
Water11,259625
1
A: 7,8-dihydroneopterin aldolase
B: 7,8-dihydroneopterin aldolase
C: 7,8-dihydroneopterin aldolase
D: 7,8-dihydroneopterin aldolase
hetero molecules

A: 7,8-dihydroneopterin aldolase
B: 7,8-dihydroneopterin aldolase
C: 7,8-dihydroneopterin aldolase
D: 7,8-dihydroneopterin aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,33328
Polymers129,0658
Non-polymers3,26720
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area28240 Å2
ΔGint-146 kcal/mol
Surface area34510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.370, 81.155, 96.514
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-467-

HOH

-
Components

#1: Protein
7,8-dihydroneopterin aldolase


Mass: 16133.166 Da / Num. of mol.: 4 / Mutation: Y53F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: y3531 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8CZR7, dihydroneopterin aldolase
#2: Chemical
ChemComp-NPR / 2-AMINO-7,8-DIHYDRO-6-(1,2,3-TRIHYDROXYPROPYL)-4(1H)-PTERIDINONE / 7,8-DIHYDRONEOPTERIN


Mass: 255.231 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H13N5O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 625 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.05 - 0.1M BisTris, 0.1-0.2 M CaCl2, 0 - 0.1M NaCl, 43 - 49% MPD
PH range: 6.2 - 6.7

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Mar 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.78→35 Å / Num. obs: 54195 / % possible obs: 99.7 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.036 / Rrim(I) all: 0.083 / Χ2: 1.013 / Net I/σ(I): 7.6 / Num. measured all: 253737
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.78-1.812.20.53526120.8080.4460.70.56398
1.81-1.842.40.46226670.8010.3620.590.58498.9
1.84-1.882.60.43126790.840.3240.5420.60699.6
1.88-1.922.80.34826310.8840.2520.4320.62499.5
1.92-1.9630.29926990.9180.2030.3640.6599.6
1.96-23.40.24926820.940.1580.2960.7399.5
2-2.053.80.2226580.950.1290.2560.95899.6
2.05-2.114.20.19326960.9650.1070.2210.84999.6
2.11-2.174.60.17326670.9760.0890.1950.89699.6
2.17-2.245.30.16227060.980.0770.180.98999.5
2.24-2.325.90.14426790.9880.0650.1580.88999.7
2.32-2.4260.12726990.9910.0560.1390.90199.9
2.42-2.536.20.1127110.9920.0480.120.962100
2.53-2.666.20.0927090.9950.0390.0991.018100
2.66-2.836.20.08127290.9950.0350.0881.059100
2.83-3.046.10.06527120.9960.0280.0710.945100
3.04-3.356.10.05427670.9970.0230.0591.015100
3.35-3.8360.0527570.9970.0220.0551.279100
3.83-4.835.70.04728070.9980.0210.0521.46899.9
4.83-354.70.04429280.9970.0220.051.73599.9

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.17refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ojo

6ojo


Resolution: 1.78→33.47 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2095 1998 3.69 %
Rwork0.1674 52104 -
obs0.169 54102 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.75 Å2 / Biso mean: 22.6337 Å2 / Biso min: 8.21 Å2
Refinement stepCycle: final / Resolution: 1.78→33.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3684 0 112 625 4421
Biso mean--27.49 34.82 -
Num. residues----468
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153928
X-RAY DIFFRACTIONf_angle_d1.295331
X-RAY DIFFRACTIONf_dihedral_angle_d20.7281415
X-RAY DIFFRACTIONf_chiral_restr0.096606
X-RAY DIFFRACTIONf_plane_restr0.008680
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.78-1.820.28191360.28483565370196
1.82-1.870.2941410.25423660380199
1.87-1.930.27941420.222937013843100
1.93-1.990.2741400.19936633803100
1.99-2.060.26481420.192136783820100
2.06-2.150.2631410.188837043845100
2.15-2.240.21281430.177437023845100
2.24-2.360.24111410.174536973838100
2.36-2.510.22761430.170837193862100
2.51-2.70.20851430.171837333876100
2.7-2.970.20941430.169137573900100
2.97-3.40.19751450.143337603905100
3.4-4.290.14131470.127138043951100
4.29-33.470.18171510.15239614112100

+
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