[English] 日本語
Yorodumi
- PDB-4nmf: Crystal structure of proline utilization A (PutA) from Geobacter ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4nmf
TitleCrystal structure of proline utilization A (PutA) from Geobacter sulfurreducens PCA inactivated by N-propargylglycine and complexed with menadione bisulfite
ComponentsProline dehydrogenase and Delta-1-pyrroline-5-carboxylate dehydrogenase
KeywordsOXIDOREDUCTASE / flavoenzyme / Rossmann fold / aldehyde dehydrogenase / flavin adenine dinucleotide / nicotinamide adenine dinucleotide / proline catabolism / substrate channeling / bifunctional enzyme / mechanism-based inactivation
Function / homology
Function and homology information


proline dehydrogenase activity / L-glutamate gamma-semialdehyde dehydrogenase / L-glutamate gamma-semialdehyde dehydrogenase activity / L-proline catabolic process to L-glutamate / cytoplasmic side of plasma membrane / DNA-binding transcription factor activity / nucleotide binding
Similarity search - Function
Proline utilization A, N-terminal / Proline utilization A N-terminal domain / 1-pyrroline-5-carboxylate dehydrogenase / Bifunctional protein PutA / Proline dehydrogenase domain / Proline dehydrogenase / : / FAD-linked oxidoreductase-like / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. ...Proline utilization A, N-terminal / Proline utilization A N-terminal domain / 1-pyrroline-5-carboxylate dehydrogenase / Bifunctional protein PutA / Proline dehydrogenase domain / Proline dehydrogenase / : / FAD-linked oxidoreductase-like / 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
Similarity search - Domain/homology
Chem-2L3 / Chem-2LB / Chem-P5F / L-glutamate gamma-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesGeobacter sulfurreducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSingh, H. / Tanner, J.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structures of the PutA peripheral membrane flavoenzyme reveal a dynamic substrate-channeling tunnel and the quinone-binding site.
Authors: Singh, H. / Arentson, B.W. / Becker, D.F. / Tanner, J.J.
History
DepositionNov 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Proline dehydrogenase and Delta-1-pyrroline-5-carboxylate dehydrogenase
B: Proline dehydrogenase and Delta-1-pyrroline-5-carboxylate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,70615
Polymers224,6492
Non-polymers3,05713
Water18,1411007
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10360 Å2
ΔGint-3 kcal/mol
Surface area66660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.594, 151.741, 176.606
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Proline dehydrogenase and Delta-1-pyrroline-5-carboxylate dehydrogenase / Proline utilization A / PutA


Mass: 112324.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter sulfurreducens (bacteria) / Strain: ATCC 51573 / DSM 12127 / PCA / Gene: putA, GSU3395 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI
References: UniProt: Q746X3, EC: 1.5.99.8, EC: 1.5.1.12, L-glutamate gamma-semialdehyde dehydrogenase

-
Non-polymers , 5 types, 1020 molecules

#2: Chemical ChemComp-P5F / N-propargylglycine-modified flavin adenine dinucleotide


Mass: 898.664 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H40N10O17P2
#3: Chemical ChemComp-2L3 / (2R)-2-methyl-1,4-dioxo-1,2,3,4-tetrahydronaphthalene-2-sulfonic acid / menadione bisulfite


Mass: 254.259 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H10O5S
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-2LB / (2S)-2-methyl-1,4-dioxo-1,2,3,4-tetrahydronaphthalene-2-sulfonic acid / menadione bisulfite


Mass: 254.259 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H10O5S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1007 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25-33% PEG550 MME, 0.05-0.2 M Bis-Tris, pH 6.4-6.5, 0.05 mM calcium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2013
RadiationMonochromator: Cryo-Cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.95→47.6 Å / Num. obs: 183582 / % possible obs: 98.5 % / Redundancy: 3.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.053 / Rrim(I) all: 0.106 / Net I/σ(I): 11.9 / Num. measured all: 691229
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.8 %

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) all% possible all
1.95-1.980.8581.83346689050.6590.4980.99797.7
10.68-47.60.01743.3469012280.9990.010.0296.1

-
Processing

Software
NameVersionClassificationNB
SCALA0.1.29data scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4NMC

4nmc


Resolution: 1.95→47.596 Å / Occupancy max: 1 / Occupancy min: 0.41 / FOM work R set: 0.8654 / SU ML: 0.2 / σ(F): 1.35 / Phase error: 20.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2026 9210 5.02 %FROM PDB ENTRY 4NME
Rwork0.1726 ---
obs0.1741 183440 98.24 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.1 Å2 / Biso mean: 21.7498 Å2 / Biso min: 6.87 Å2
Refinement stepCycle: LAST / Resolution: 1.95→47.596 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15159 0 195 1007 16361
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00715743
X-RAY DIFFRACTIONf_angle_d1.06321351
X-RAY DIFFRACTIONf_chiral_restr0.072319
X-RAY DIFFRACTIONf_plane_restr0.0052775
X-RAY DIFFRACTIONf_dihedral_angle_d14.3025832
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-1.97240.28392850.24845635592097
1.9724-1.99560.26253210.229458226143100
1.9956-2.01990.28443100.220757926102100
2.0199-2.04550.27673350.22795799613499
2.0455-2.07240.27442810.22495858613999
2.0724-2.10080.25362950.21655817611299
2.1008-2.13080.26413230.20945773609699
2.1308-2.16260.24632880.20675772606098
2.1626-2.19640.24463200.20315610593096
2.1964-2.23240.22232980.19175835613399
2.2324-2.27090.28443180.2145799611799
2.2709-2.31220.2182860.182958306116100
2.3122-2.35670.22842850.174459076192100
2.3567-2.40480.21253030.171358596162100
2.4048-2.45710.22713100.177158666176100
2.4571-2.51420.22683230.17535845616899
2.5142-2.57710.19852900.17585875616599
2.5771-2.64680.20733130.1715816612999
2.6468-2.72470.21883130.17525781609498
2.7247-2.81260.22593040.18335654595896
2.8126-2.91310.25193090.18525755606498
2.9131-3.02970.20813220.18495885620799
3.0297-3.16760.20643320.18125808614099
3.1676-3.33450.19682830.18075888617199
3.3345-3.54340.17573140.16835865617998
3.5434-3.81690.18823330.15815826615998
3.8169-4.20080.15462950.1395481577692
4.2008-4.80810.14472920.12565929622198
4.8081-6.05580.15243220.14745951627398
6.0558-47.61070.16933070.15335897620494

+
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