[English] 日本語
Yorodumi
- PDB-4qpc: Crystal structure of the hydrolase domain of 10-formyltetrahydrof... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4qpc
TitleCrystal structure of the hydrolase domain of 10-formyltetrahydrofolate dehydrogenase (Y200A) from zebrafish
Components10-formyltetrahydrofolate dehydrogenase
KeywordsOXIDOREDUCTASE / 10-Formyltetrahydrofolate dehydrogenase / hydrolase domain / catalysis
Function / homology
Function and homology information


neuromast deposition / Metabolism of folate and pterines / formyltetrahydrofolate dehydrogenase / formyltetrahydrofolate dehydrogenase activity / 10-formyltetrahydrofolate catabolic process / embryonic viscerocranium morphogenesis / aldehyde dehydrogenase (NAD+) activity / neural crest cell migration / biosynthetic process / gastrulation ...neuromast deposition / Metabolism of folate and pterines / formyltetrahydrofolate dehydrogenase / formyltetrahydrofolate dehydrogenase activity / 10-formyltetrahydrofolate catabolic process / embryonic viscerocranium morphogenesis / aldehyde dehydrogenase (NAD+) activity / neural crest cell migration / biosynthetic process / gastrulation / one-carbon metabolic process / heart development / hydrolase activity / cytoplasm
Similarity search - Function
Formyl transferase, C-terminal domain / Methionyl-tRNA Fmet Formyltransferase; Chain A, domain 2 / 10-formyltetrahydrofolate dehydrogenase / Formyl transferase, C-terminal domain superfamily / Formyl transferase, C-terminal / Formyl transferase, C-terminal domain / Formyl transferase-like, C-terminal domain superfamily / Formyl transferase, N-terminal domain / Phosphoribosylglycinamide formyltransferase, active site / Phosphoribosylglycinamide formyltransferase active site. ...Formyl transferase, C-terminal domain / Methionyl-tRNA Fmet Formyltransferase; Chain A, domain 2 / 10-formyltetrahydrofolate dehydrogenase / Formyl transferase, C-terminal domain superfamily / Formyl transferase, C-terminal / Formyl transferase, C-terminal domain / Formyl transferase-like, C-terminal domain superfamily / Formyl transferase, N-terminal domain / Phosphoribosylglycinamide formyltransferase, active site / Phosphoribosylglycinamide formyltransferase active site. / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
10-formyltetrahydrofolate dehydrogenase
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.902 Å
AuthorsLin, C.C. / Chen, C.J. / Fu, T.F. / Chuankhayan, P. / Kao, T.T. / Chang, W.N.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structures of the hydrolase domain of zebrafish 10-formyltetrahydrofolate dehydrogenase and its complexes reveal a complete set of key residues for hydrolysis and product inhibition.
Authors: Lin, C.C. / Chuankhayan, P. / Chang, W.N. / Kao, T.T. / Guan, H.H. / Fun, H.K. / Nakagawa, A. / Fu, T.F. / Chen, C.J.
History
DepositionJun 23, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation / struct_ref_seq_dif
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _struct_ref_seq_dif.details
Revision 1.2Nov 8, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 10-formyltetrahydrofolate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)35,3641
Polymers35,3641
Non-polymers00
Water6,215345
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: 10-formyltetrahydrofolate dehydrogenase

A: 10-formyltetrahydrofolate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)70,7292
Polymers70,7292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area1630 Å2
ΔGint-9 kcal/mol
Surface area28400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.460, 53.959, 60.877
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-690-

HOH

21A-721-

HOH

31A-722-

HOH

-
Components

#1: Protein 10-formyltetrahydrofolate dehydrogenase


Mass: 35364.344 Da / Num. of mol.: 1 / Fragment: UNP residues 1-311 / Mutation: Y200A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: aldh1l1 / Production host: Escherichia coli (E. coli)
References: UniProt: E3NZ06, formyltetrahydrofolate dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / 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: 2.43 Å3/Da / Density % sol: 49.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1~0.2M Bis-Tris pH 5.5, 25~29%(w/v) PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 13, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 27430 / Num. obs: 27430 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.9→1.97 Å / % possible all: 99.8

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TS4

4ts4


Resolution: 1.902→24 Å / SU ML: 0.18 / σ(F): 1.33 / Phase error: 23.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2247 1376 5.04 %RANDOM
Rwork0.2035 ---
obs0.2046 27326 98.57 %-
all-27430 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.134 Å2 / ksol: 0.312 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.9419 Å2-0 Å2-0 Å2
2--4.6307 Å2-0 Å2
3----0.6887 Å2
Refinement stepCycle: LAST / Resolution: 1.902→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2408 0 0 345 2753
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062467
X-RAY DIFFRACTIONf_angle_d1.0533337
X-RAY DIFFRACTIONf_dihedral_angle_d15.367920
X-RAY DIFFRACTIONf_chiral_restr0.067356
X-RAY DIFFRACTIONf_plane_restr0.005437
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9021-1.970.37371260.3274252098
1.97-2.04890.28091320.22262589100
2.0489-2.14210.21841360.20872596100
2.1421-2.25490.28741250.2501258699
2.2549-2.39610.30361430.2273253699
2.3961-2.58090.22691500.20022615100
2.5809-2.84020.22841350.20062629100
2.8402-3.25040.20841520.20422637100
3.2504-4.09180.19971260.1806245492
4.0918-24.00180.17911510.1753278899
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)
11.83150.8880.31872.932-0.49732.03690.0647-0.2627-0.51710.1458-0.3085-0.78060.41870.42990.10630.26270.0371-0.00320.26310.1290.357414.63337.869521.0329
23.19121.5996-0.62711.7223-0.32510.83870.1192-0.20440.03870.1561-0.0393-0.0133-0.01690.0565-0.07640.11680.0107-0.00490.10770.00810.096912.732127.066715.6642
34.75381.5948-0.45621.1891-0.39910.9982-0.00290.2764-0.3293-0.04950.0212-0.16780.06090.1518-0.01840.15290.03310.00480.0995-0.04320.142224.008929.06467.5944
45.33380.4254-0.79450.1664-0.7834.72310.2287-0.24150.75020.2383-0.1012-0.172-0.63170.3961-0.01850.2425-0.03830.03880.1887-0.0220.25440.280543.16379.7091
56.4081-0.2710.89653.3283-0.71756.06870.0662-0.27250.11960.2672-0.0911-0.24290.20960.61680.00590.1508-0.00430.01750.2079-0.01740.121441.019139.091113.8231
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:106)
2X-RAY DIFFRACTION2chain 'A' and (resseq 107:184)
3X-RAY DIFFRACTION3chain 'A' and (resseq 185:239)
4X-RAY DIFFRACTION4chain 'A' and (resseq 240:270)
5X-RAY DIFFRACTION5chain 'A' and (resseq 271:308)

+
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