[English] 日本語
Yorodumi
- PDB-4mpd: Staphyloferrin B precursor biosynthetic enzyme SbnB bound a-ketog... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4mpd
TitleStaphyloferrin B precursor biosynthetic enzyme SbnB bound a-ketoglutarate and NAD+
ComponentsPutative ornithine cyclodeaminase
KeywordsOXIDOREDUCTASE / siderophore / iron / L-Dap synthesis / ACEGA dehydrogenase
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor / siderophore biosynthetic process / nucleotide binding
Similarity search - Function
2,3-diaminopropionate biosynthesis protein SbnB / ornithine cyclodeaminase, domain 1 / ornithine cyclodeaminase, domain 1 / Ornithine cyclodeaminase/mu-crystallin / Ornithine cyclodeaminase, N-terminal / Ornithine cyclodeaminase/mu-crystallin family / NAD(P)-binding Rossmann-like Domain / Ig-like domain profile. / Immunoglobulin-like domain / NAD(P)-binding domain superfamily ...2,3-diaminopropionate biosynthesis protein SbnB / ornithine cyclodeaminase, domain 1 / ornithine cyclodeaminase, domain 1 / Ornithine cyclodeaminase/mu-crystallin / Ornithine cyclodeaminase, N-terminal / Ornithine cyclodeaminase/mu-crystallin family / NAD(P)-binding Rossmann-like Domain / Ig-like domain profile. / Immunoglobulin-like domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDIC FORM) / 2,3-diaminopropionate biosynthesis protein SbnB / Putative ornithine cyclodeaminase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.101 Å
AuthorsKobylarz, M.J. / Murphy, M.E.P.
CitationJournal: Chem.Biol. / Year: 2014
Title: Synthesis of L-2,3-diaminopropionic Acid, a siderophore and antibiotic precursor.
Authors: Kobylarz, M.J. / Grigg, J.C. / Takayama, S.J. / Rai, D.K. / Heinrichs, D.E. / Murphy, M.E.
History
DepositionSep 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative ornithine cyclodeaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8823
Polymers38,0731
Non-polymers8102
Water1,35175
1
A: Putative ornithine cyclodeaminase
hetero molecules

A: Putative ornithine cyclodeaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7656
Polymers76,1462
Non-polymers1,6194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area7370 Å2
ΔGint-32 kcal/mol
Surface area24170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.931, 61.931, 151.718
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Putative ornithine cyclodeaminase /


Mass: 38072.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: NEWMAN / Gene: sbnB / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8NYS7, UniProt: A0A0H3K9Y6*PLUS
#2: Chemical ChemComp-NAJ / NICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDIC FORM) / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 1.91 Å3/Da / Density % sol: 35.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Hepes, 0.2 M MgCl2, 29-33% PEG 400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 18, 2013
RadiationMonochromator: Rigaku VariMax VHF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→27.25 Å / Num. obs: 15508 / % possible obs: 85.9 % / Observed criterion σ(I): 4.5 / Redundancy: 6.9 % / Biso Wilson estimate: 27.08 Å2 / Rmerge(I) obs: 0.108 / Χ2: 1.115 / Net I/σ(I): 8.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.146.90.4648111.046190.4
2.14-2.187.80.4358301.131196.4
2.18-2.228.20.447881.068190.7
2.22-2.268.10.4198161.101193.2
2.26-2.318.30.3667931.13188.7
2.31-2.378.20.3447891.118189.4
2.37-2.4280.3277781.187189.1
2.42-2.498.10.3097431.117183.8
2.49-2.567.80.2747421.126183.8
2.56-2.657.50.2627341.156183
2.65-2.747.30.2277091.267179.8
2.74-2.856.90.2037021.185178.5
2.85-2.986.50.176931.144176.8
2.98-3.1460.1426721.145174.8
3.14-3.335.70.0996711.134174.4
3.33-3.594.90.0776801.05174.5
3.59-3.954.20.0677441.06181.8
3.95-4.5240.0558801.075194.6
4.52-5.75.50.0499400.977198.2
5.7-508.10.0519931.048194.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.5.3phasing
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
PHENIX1.8.2_1309refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.101→27.249 Å / Occupancy max: 1 / Occupancy min: 0.03 / FOM work R set: 0.7943 / SU ML: 0.27 / σ(F): 1.33 / Phase error: 26.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2658 1505 9.77 %RANDOM
Rwork0.2293 ---
obs0.2329 15406 85.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.14 Å2 / Biso mean: 34.1003 Å2 / Biso min: 15.27 Å2
Refinement stepCycle: LAST / Resolution: 2.101→27.249 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2513 0 54 75 2642
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032622
X-RAY DIFFRACTIONf_angle_d0.7013557
X-RAY DIFFRACTIONf_chiral_restr0.052400
X-RAY DIFFRACTIONf_plane_restr0.002459
X-RAY DIFFRACTIONf_dihedral_angle_d14.472974
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1009-2.16870.28191440.26321332147693
2.1687-2.24610.26561470.24911318146592
2.2461-2.3360.31441470.25781300144791
2.336-2.44230.30891350.26071264139988
2.4423-2.5710.26951310.24351224135583
2.571-2.73190.29161230.2721164128781
2.7319-2.94260.35251170.27611119123676
2.9426-3.23830.28731140.24731114122875
3.2383-3.70590.2191150.21471112122774
3.7059-4.66520.21921590.19181366152591
4.6652-27.2510.27691730.21291588176198
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.62590.4307-2.07191.38360.192.6032-0.17830.46-0.12220.20060.0075-0.174-0.158-0.07320.14690.2646-0.0188-0.07360.25440.04670.1945-23.829222.7176-11.1396
21.19510.5641-1.61470.5235-1.31375.8302-0.0241-0.06660.45120.1545-0.1437-0.179-0.12591.3235-0.23350.3440.0005-0.07510.36790.05690.6061-17.464837.1148-3.494
34.8125-0.4976-0.14682.89150.40843.4030.0073-0.32670.37180.2509-0.0432-0.79880.04850.24220.01050.21110.0455-0.06080.2379-0.04370.3925-24.303228.32240.8709
43.72470.4370.25493.2522-0.06391.6543-0.0671-0.1171-0.32250.18740.10640.01950.1030.0632-0.04230.19550.0337-0.00160.1618-0.0130.1858-2.058917.4892-3.7425
53.6472.08694.11643.82413.25465.4206-0.1979-0.25050.4449-0.42530.04580.0951-0.9352-0.2530.19850.40830.0728-0.030.28650.00420.38350.378740.0122-6.4844
65.9268-0.86343.00194.1038-0.0834.30070.15750.82310.7393-0.8428-0.4238-0.2998-0.00020.74310.20660.3172-0.00550.03140.37220.03960.16911.857428.3628-19.1721
72.4581-1.0892-0.8953-0.26810.50950.55270.03110.33580.4762-0.0586-0.0736-0.01680.1416-0.12890.00550.2672-0.0251-0.01660.2840.06750.3474-24.881126.3609-10.1542
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 36 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 74 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 75 through 115 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 116 through 253 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 254 through 283 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 284 through 301 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 302 through 336 )A0

+
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