[English] 日本語
Yorodumi
- PDB-1zwj: X-ray structure of galt-like protein from arabidopsis thaliana AT... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1zwj
TitleX-ray structure of galt-like protein from arabidopsis thaliana AT5G18200
Componentsputative galactose-1-phosphate uridyl transferase
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / GALT / AT5G18200 / PROTEIN STRUCTURE INITIATIVE / PSI / CESG / Center for Eukaryotic Structural Genomics
Function / homology
Function and homology information


ribose-5-phosphate adenylyltransferase activity / positive regulation of cellular response to phosphate starvation / UDP-glucose:hexose-1-phosphate uridylyltransferase activity / galactose metabolic process / nucleotidyltransferase activity / ADP binding / glucose metabolic process / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / carbohydrate metabolic process / zinc ion binding
Similarity search - Function
: / Galactose-1-phosphate uridyl transferase, N-terminal / Galactose-1-phosphate uridyl transferase, C-terminal / Galactose-1-phosphate uridyl transferase, N-terminal domain / Galactose-1-phosphate uridyl transferase, C-terminal domain / Galactose-1-phosphate uridyl transferase, class I / HIT-like / HIT family, subunit A / HIT-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADP-glucose phosphorylase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT, SAD / SAD / Resolution: 2.3 Å
AuthorsWesenberg, G.E. / Smith, D.W. / Phillips Jr., G.N. / McCoy, J.G. / Johnson, K.A. / Bitto, E. / Bingman, C.A. / Allard, S.T.M. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Biochemistry / Year: 2006
Title: Structure and Mechanism of an ADP-Glucose Phosphorylase from Arabidopsis thaliana
Authors: MCCOY, J.G. / ARABSHAHI, A. / BITTO, E. / BINGMAN, C.A. / RUZICKA, F.J. / FREY, P.A. / PHILLIPS JR., G.N.
History
DepositionJun 3, 2005Deposition site: RCSB / Processing site: RCSB
SupersessionJun 14, 2005ID: 1VKV
Revision 1.0Jun 14, 2005Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: putative galactose-1-phosphate uridyl transferase
B: putative galactose-1-phosphate uridyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,3686
Polymers78,1062
Non-polymers2624
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-33 kcal/mol
Surface area23620 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)59.984, 95.535, 110.522
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is likely a dimer with one biological unit in the asymmetric unit

-
Components

#1: Protein putative galactose-1-phosphate uridyl transferase


Mass: 39053.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g18200 / Plasmid: PVP 13 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA / References: UniProt: Q9FK51
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 10 MG/ML PROTEIN, 20% PEG 2K, 0.2M SODIUM CHLORIDE, 0.1M MES-ACETATE, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 14-ID-B10.9786
SYNCHROTRONAPS 32-ID20.9791
SYNCHROTRONAPS 32-ID30.9791
Detector
TypeIDDetectorDateDetails
MAR CCD 165 mm1CCDFeb 11, 2004bent cylindrical Si-mirror (Rh coating)
MAR CCD 165 mm2CCDApr 4, 2004Rh Mirror
MAR CCD 165 mm3CCDApr 4, 2004Rh Mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Diamond (111) double-crystal monochromatorSINGLE WAVELENGTHMx-ray1
2Diamond 111SINGLE WAVELENGTHMx-ray1
3Diamond 111SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97861
20.97911
Reflection

D res low: 50 Å

Redundancy (%)IDNumberRmerge(I) obsΧ2D res high (Å)% possible obs
6.41275750.0440.8582.395.6
7.62202510.1071.1683.299.8
7.53201370.0991.073.299.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.675098.110.0231.0616.8
4.55.6799.710.0230.7777.2
3.934.599.710.0260.747.3
3.573.9399.710.0340.7877.4
3.323.5799.210.0460.8427.3
3.123.3299.310.0680.8587
2.973.1298.910.0920.8976.8
2.842.9798.310.120.8776.5
2.732.849910.150.96.1
2.632.739710.1840.8855.9
2.552.6395.310.2350.875.8
2.482.5593.210.2710.8615.7
2.412.4891.410.320.8575.6
2.352.4183.510.40.8345.5
2.32.3580.410.4060.8335.1
7.885097.620.0591.0536
6.267.8810020.0731.2637.3
5.476.2610020.0821.3717.4
4.975.4710020.0841.3397.5
4.614.9710020.0841.3537.5
4.344.6110020.0921.3677.6
4.134.3410020.1051.3397.6
3.954.1310020.1141.2727.8
3.793.9510020.1311.2257.8
3.663.7910020.1431.077.8
3.553.6610020.1551.1957.8
3.453.5510020.1861.0837.8
3.363.4510020.2091.0147.8
3.273.3610020.2570.8627.8
3.23.2710020.2840.7447.8
7.88509730.0520.8615.4
6.267.8899.330.0631.0116.9
5.476.2699.930.071.0987.2
4.975.4710030.0731.2337.3
4.614.9710030.0721.0337.4
4.344.6110030.0771.0417.5
4.134.3410030.0931.397.6
3.954.1310030.1031.1277.8
3.793.9510030.1211.1397.8
3.663.7910030.1391.1737.8
3.553.6610030.1461.1917.9
3.453.5510030.1821.0767.9
3.363.4510030.2090.9787.9
3.273.3610030.260.8867.8
3.23.2710030.3050.7627.8
ReflectionResolution: 2.3→50 Å / Num. obs: 27575 / % possible obs: 95.6 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.044 / Χ2: 0.858 / Net I/σ(I): 24.03
Reflection shell

Diffraction-ID: 1,2,3

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsΧ2% possible all
2.3-2.3580.45.10.4063.64615130.83380.4
2.35-2.4183.55.50.415740.834
2.41-2.4891.45.60.3217240.857
2.48-2.5593.25.70.27117500.861
2.55-2.6395.35.80.23518320.87
2.63-2.73975.90.18418420.885
2.73-2.84996.10.1518630.9
2.84-2.9798.36.50.1218930.877
2.97-3.1298.96.80.09218670.897
3.12-3.3299.370.06819170.858
3.32-3.5799.27.30.04619100.842
3.57-3.9399.77.40.03419300.787
3.93-4.599.77.30.02619330.74
4.5-5.6799.77.20.02319660.777
5.67-5098.16.80.02320611.061

-
Phasing

PhasingMethod: SAD
Phasing MADD res high: 3.49 Å / D res low: 40.19 Å / FOM : 0.321 / FOM acentric: 0.353 / FOM centric: 0 / Reflection: 15287
Phasing MAD setR cullis: 0.673 / R cullis acentric: 0.64 / R cullis centric: 10 / R kraut: 0.032 / R kraut acentric: 0.032 / R kraut centric: 0.035 / Highest resolution: 3.49 Å / Lowest resolution: 40.19 Å / FOM : 0.319 / FOM acentric: 0.351 / FOM centric: 0 / Loc: 5.185 / Loc acentric: 5.18 / Loc centric: 5.282 / Power: 1.634 kW / Power acentric: 1.604 / Power centric: 1.903
Phasing MAD setWavelength: 0.97908 Å / Atom type: SE / F double prime refined: 0.68 / F prime refined: -10
Phasing MAD set shell

ID: 1 / R cullis centric: 10 / FOM centric: 0

Resolution (Å)R cullisR cullis acentricR krautR kraut acentricR kraut centricFOM FOM acentricLocLoc acentricLoc centricPower (kW)Power acentricPower centric
6.97-40.190.5310.4820.0360.0340.0480.4040.4925.8785.8875.922.432.3812.645
5.54-6.970.5290.50.040.040.040.4290.4814.8474.854.8752.2922.3042.185
4.84-5.540.6110.5810.0320.0310.0340.3840.4244.8494.8524.8811.8681.8831.728
4.4-4.840.7070.6790.0270.0270.0250.3430.3735.2575.2585.2731.4661.4581.552
4.08-4.40.7670.7380.0280.0280.0240.3060.3315.315.3125.3271.1991.21.191
3.84-4.080.8390.8080.030.030.0240.260.285.0765.0785.0931.0521.0580.974
3.65-3.840.8560.8280.0330.0340.0230.2220.2375.0715.0735.090.9220.9220.928
3.49-3.650.9130.8840.0360.0360.0310.1960.2095.2185.2195.2290.7810.7790.801
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
118.407460.942545.5874SE75.45381
213.7660.030449.9678SE54.6521
312.362529.862216.7179SE60.49741
435.564531.159330.9156SE70.83011
521.532833.826330.1783SE70.97991
69.2736447.115442.495SE77.1471
7-4.8450947.03744.9608SE74.76211
817.151325.356617.9272SE89.45651
910.720645.34762.6713SE124.4261
1028.82188.5382470.0125SE92.37971
112.205739.9755471.0682SE80.64431
1219.932913.971634.0314SE99.03871
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflection
6.97-40.190.40490.489301907
5.54-6.970.4310.48301940
4.84-5.540.38860.428401936
4.4-4.840.34660.376101925
4.08-4.40.30790.332301936
3.84-4.080.26030.280301935
3.65-3.840.22180.237101927
3.49-3.650.19520.208101781

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
CNS1.1refinement
PDB_EXTRACT1.6data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT, SAD
Starting model: PDB ENTRY 1GUP

1gup


Resolution: 2.3→27.59 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.269 2581 10 %RANDOM
Rwork0.215 ---
all-28839 --
obs-25918 89.9 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 37.3753 Å2 / ksol: 0.327623 e/Å3
Displacement parametersBiso max: 100.34 Å2 / Biso mean: 47.15 Å2 / Biso min: 19.99 Å2
Baniso -1Baniso -2Baniso -3
1-5.8 Å20 Å20 Å2
2--7.23 Å20 Å2
3----13.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.31 Å
Luzzati d res high-2.3
Refinement stepCycle: LAST / Resolution: 2.3→27.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4756 0 4 225 4985
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.94
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.3-2.410.38326410.70.3122090.0243558247369.5
2.41-2.530.3292659.40.26625480.023519281379.9
2.53-2.690.3132909.30.26228200.0183581311086.8
2.69-2.90.3323069.50.25429040.0193570321089.9
2.9-3.190.31934610.30.24330250.0173576337194.3
3.19-3.650.27237410.50.20831890.0143617356398.5
3.65-4.60.24361100.19132440.0133640360599
4.6-27.590.2293759.90.19133980.0123797377399.4
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top

+
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