[English] 日本語
Yorodumi
- PDB-3ggg: The crystal structure of A. aeolicus prephenate dehydrogenase in ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ggg
TitleThe crystal structure of A. aeolicus prephenate dehydrogenase in complex with tyrosine and NAD+
ComponentsPrephenate dehydrogenase
KeywordsOXIDOREDUCTASE / dinucleotide binding fold / beta-alpha / Tyrosine-bound / NAD
Function / homology
Function and homology information


prephenate dehydrogenase (NADP+) activity / prephenate dehydrogenase (NAD+) activity / tyrosine biosynthetic process / NAD+ binding
Similarity search - Function
Prephenate dehydrogenase, dimerization domain / Prephenate dehydrogenase, dimerization domain / 6-phosphogluconate dehydrogenase C-terminal fold / 6-phosphogluconate dehydrogenase C-terminal like domain / Prephenate dehydrogenase, nucleotide-binding domain / Prephenate dehydrogenase / Prephenate dehydrogenase, nucleotide-binding domain / Prephenate/arogenate dehydrogenase domain profile. / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain ...Prephenate dehydrogenase, dimerization domain / Prephenate dehydrogenase, dimerization domain / 6-phosphogluconate dehydrogenase C-terminal fold / 6-phosphogluconate dehydrogenase C-terminal like domain / Prephenate dehydrogenase, nucleotide-binding domain / Prephenate dehydrogenase / Prephenate dehydrogenase, nucleotide-binding domain / Prephenate/arogenate dehydrogenase domain profile. / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / TYROSINE / Prephenate dehydrogenase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsSun, W. / Shahinas, D. / Christendat, D.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: The Crystal Structure of Aquifex aeolicus Prephenate Dehydrogenase Reveals the Mode of Tyrosine Inhibition.
Authors: Sun, W. / Shahinas, D. / Bonvin, J. / Hou, W. / Kimber, M.S. / Turnbull, J. / Christendat, D.
History
DepositionFeb 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Sep 6, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
D: Prephenate dehydrogenase
A: Prephenate dehydrogenase
B: Prephenate dehydrogenase
C: Prephenate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,07110
Polymers141,0554
Non-polymers3,0166
Water2,360131
1
D: Prephenate dehydrogenase
B: Prephenate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0365
Polymers70,5282
Non-polymers1,5083
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10390 Å2
ΔGint-88 kcal/mol
Surface area24620 Å2
MethodPISA
2
A: Prephenate dehydrogenase
C: Prephenate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0365
Polymers70,5282
Non-polymers1,5083
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9930 Å2
ΔGint-89 kcal/mol
Surface area23270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.431, 93.691, 163.656
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Prephenate dehydrogenase /


Mass: 35263.773 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: aq_1755, tyrA / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O67636
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-TYR / TYROSINE / Tyrosine


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.16 Å3/Da / Density % sol: 43.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 48% MPD, 100 mM HEPES, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: SBC-2 / Detector: CCD / Date: Jul 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.2→46.85 Å / Num. all: 62250 / Num. obs: 61690 / % possible obs: 99.1 % / Observed criterion σ(I): 2.5 / Redundancy: 8.9 % / Rsym value: 0.07 / Net I/σ(I): 40
Reflection shellResolution: 2.2→2.262 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.311 / % possible all: 93.1

-
Processing

Software
NameVersionClassification
HKL-3000data collection
AMoREphasing
REFMAC5.5.0072refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2g5c

2g5c


Resolution: 2.21→46.85 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.919 / SU B: 13.013 / SU ML: 0.162 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.281 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25419 1913 3.1 %RANDOM
Rwork0.19291 ---
obs0.1948 59708 98.86 %-
all-59735 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.613 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2---0.12 Å2-0 Å2
3---0.25 Å2
Refinement stepCycle: LAST / Resolution: 2.21→46.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9062 0 200 131 9393
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0229453
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9922.00612749
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.61651145
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.12824.271377
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.008151772
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9321543
X-RAY DIFFRACTIONr_chiral_restr0.1420.21433
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216819
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.9431.55692
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.67329211
X-RAY DIFFRACTIONr_scbond_it3.03733761
X-RAY DIFFRACTIONr_scangle_it4.644.53538
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.21→2.262 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 116 -
Rwork0.248 4012 -
obs--90.51 %
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)
11.881-0.4229-0.33475.5347-0.11812.9795-0.041-0.07710.17560.3751-0.0841-0.4156-0.11250.11690.12510.2612-0.0033-0.02360.16380.05860.179717.684-2.723-41.972
22.53330.2791-0.71293.9373-0.73411.6407-0.0026-0.00060.4021-0.07170.09-0.1262-0.23510.0281-0.08740.194-0.0094-0.00230.1552-0.01590.224426.02420.867-14.135
33.6234-1.022-0.81434.5930.62911.43760.0321-0.001-0.1591-0.1198-0.01660.02210.14760.037-0.01550.3008-0.02580.06560.18210.00230.029327.717-58.333-54.286
43.94531.06680.56053.76450.2162.285-0.08460.3098-0.1963-0.35130.10830.00120.1838-0.1781-0.02370.2926-0.00740.05580.26980.01420.091411.137-35.319-14.699
51.7148-1.7013-0.12027.1060.5290.36930.18760.12760.0176-0.7809-0.27330.4617-0.0757-0.12940.08570.34140.038-0.01880.2949-0.02360.062612.045-31.215-57.424
61.74291.273-0.31896.6207-0.7121.0333-0.0238-0.1149-0.01420.43620.0124-0.0444-0.0199-0.06270.01140.16820.0179-0.00850.25510.00770.002619.139-6.194-1.222
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 205
2X-RAY DIFFRACTION2B18 - 205
3X-RAY DIFFRACTION3C25 - 205
4X-RAY DIFFRACTION4D18 - 205
5X-RAY DIFFRACTION5A206 - 310
6X-RAY DIFFRACTION5C206 - 305
7X-RAY DIFFRACTION6B206 - 307
8X-RAY DIFFRACTION6D206 - 310

+
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