[English] 日本語
Yorodumi
- PDB-4r01: Crystal structure of SP1627, a putative NADH-flavin reductase, fr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4r01
TitleCrystal structure of SP1627, a putative NADH-flavin reductase, from Streptococcus pneumoniae TIGR4
Componentsputative NADH-flavin reductase
KeywordsOXIDOREDUCTASE / structural genomics / CSGID / Center for Structural Genomics of Infectious Diseases / NIAID / National Institute for Allergy and Infectious Diseases / alpha/beta fold / NAD(P) dinucleotide-binding Rossmann fold / putative NADH-flavin reductase / putative oxidoreductase
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor
Similarity search - Function
: / NAD(P)H-binding / NAD(P)-binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NAD(P)-binding domain-containing protein / NAD(P)-bd_dom domain-containing protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae TIGR4 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsStogios, P.J. / Onopriyenko, O. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of SP1627, a putative NADH-flavin reductase, from Streptococcus pneumoniae TIGR4
Authors: Stogios, P.J. / Onopriyenko, O. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJul 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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
A: putative NADH-flavin reductase
B: putative NADH-flavin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4809
Polymers46,0502
Non-polymers4307
Water2,954164
1
A: putative NADH-flavin reductase
B: putative NADH-flavin reductase
hetero molecules

A: putative NADH-flavin reductase
B: putative NADH-flavin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,96018
Polymers92,1004
Non-polymers86014
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area7850 Å2
ΔGint-180 kcal/mol
Surface area34970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.030, 82.960, 43.790
Angle α, β, γ (deg.)90.00, 105.56, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-424-

HOH

21B-470-

HOH

-
Components

#1: Protein putative NADH-flavin reductase


Mass: 23025.029 Da / Num. of mol.: 2 / Fragment: SP1627
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae TIGR4 (bacteria)
Strain: TIGR4 / Gene: SP_1627 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q97PI8, UniProt: A0A0H2UR89*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 3.04 Å3/Da / Density % sol: 59.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2 M Ammonium Sulfate, 0.1 M Bis-Tris Propane, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 10, 2014
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. obs: 29142 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 2.7 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 25.55
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.15 / % possible all: 96.7

-
Processing

Software
NameVersionClassification
HKL-3000data collection
BALBESphasing
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H2S

3h2s


Resolution: 2.4→29.577 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 27.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2418 1384 6.83 %random
Rwork0.1855 ---
obs0.1893 20249 93.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→29.577 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3246 0 19 164 3429
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053319
X-RAY DIFFRACTIONf_angle_d0.7874492
X-RAY DIFFRACTIONf_dihedral_angle_d14.7371222
X-RAY DIFFRACTIONf_chiral_restr0.032521
X-RAY DIFFRACTIONf_plane_restr0.004577
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.48580.34361340.26351804X-RAY DIFFRACTION90
2.4858-2.58520.30781350.26781827X-RAY DIFFRACTION89
2.5852-2.70280.32831320.25471821X-RAY DIFFRACTION93
2.7028-2.84520.33351380.2421865X-RAY DIFFRACTION93
2.8452-3.02330.33221390.23971897X-RAY DIFFRACTION94
3.0233-3.25650.26851410.22841887X-RAY DIFFRACTION95
3.2565-3.58370.25961450.1871936X-RAY DIFFRACTION95
3.5837-4.10110.21451410.15671950X-RAY DIFFRACTION96
4.1011-5.16240.16681430.1371939X-RAY DIFFRACTION96
5.1624-29.57920.20031360.15141939X-RAY DIFFRACTION93
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)
14.7486-1.45780.83025.785-1.4075.72310.2293-0.003-1.0076-0.3233-0.8496-0.50930.23230.70820.56620.32130.07480.06710.39610.11530.579724.5621-3.129215.238
25.8989-0.305-2.62391.3432-1.03826.67420.084-0.1956-0.8059-0.1169-0.17240.02680.16290.50390.15960.40010.12440.03190.35580.08520.631628.6845-2.123415.3993
39.2932-2.66340.43393.944-4.7456.6455-0.55280.37-0.10870.94430.3278-0.3101-0.31330.6480.01180.38380.10460.00920.44-0.01960.42624.25673.681310.0061
44.809-0.8491-0.47741.95330.09912.57830.12220.4443-0.4154-0.2255-0.2656-0.08490.15810.05070.14370.3030.04590.00320.2453-0.02130.325310.00853.822711.1461
58.3536-3.5355-3.11039.73770.43976.1994-0.42950.48970.4544-0.22150.4627-0.2547-0.52140.1907-0.10890.3436-0.127-0.02390.31790.05340.507818.728935.760328.1046
66.82781.2907-0.6086.8429-0.44213.19760.0114-0.05240.5936-0.15360.1596-0.338-0.16910.1637-0.17910.3281-0.1261-0.04270.3565-0.00320.405624.081234.029729.1651
77.10844.90154.93058.08256.13624.60530.0118-0.524-0.18760.4556-0.0108-0.15550.10070.2109-0.07790.3076-0.0306-0.03040.37620.08680.343820.032620.103633.1436
85.45091.59520.47443.83380.14152.23160.0101-0.380.49630.1342-0.05420.1708-0.1047-0.17290.04550.2613-0.010.01280.3429-0.02810.21244.287327.998533.2546
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 0:11 )A0 - 11
2X-RAY DIFFRACTION2( CHAIN A AND RESID 12:54 )A12 - 54
3X-RAY DIFFRACTION3( CHAIN A AND RESID 55:71 )A55 - 71
4X-RAY DIFFRACTION4( CHAIN A AND RESID 72:209 )A72 - 209
5X-RAY DIFFRACTION5( CHAIN B AND RESID 0:16 )B0 - 16
6X-RAY DIFFRACTION6( CHAIN B AND RESID 17:67 )B17 - 67
7X-RAY DIFFRACTION7( CHAIN B AND RESID 68:91 )B68 - 91
8X-RAY DIFFRACTION8( CHAIN B AND RESID 92:209 )B92 - 209

+
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