[English] 日本語
Yorodumi
- PDB-4jay: Crystal structure of P. aeruginosa MurB in complex with NADP+ -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4jay
TitleCrystal structure of P. aeruginosa MurB in complex with NADP+
ComponentsUDP-N-acetylenolpyruvoylglucosamine reductase
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


UDP-N-acetylmuramate dehydrogenase / UDP-N-acetylmuramate dehydrogenase activity / peptidoglycan biosynthetic process / FAD binding / cell wall organization / flavin adenine dinucleotide binding / regulation of cell shape / cell division / cytosol
Similarity search - Function
Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 1 / UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain / UDP-N-acetylenolpyruvoylglucosamine reductase / UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal / UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain superfamily / UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 ...Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 1 / UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain / UDP-N-acetylenolpyruvoylglucosamine reductase / UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal / UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain superfamily / UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding, type PCMH, subdomain 1 / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / : / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / UDP-N-acetylenolpyruvoylglucosamine reductase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsChen, M.W. / Lohkamp, B. / Schnell, R. / Lescar, J. / Schneider, G.
CitationJournal: Plos One / Year: 2013
Title: Substrate Channel Flexibility in Pseudomonas aeruginosa MurB Accommodates Two Distinct Substrates.
Authors: Chen, M.W. / Lohkamp, B. / Schnell, R. / Lescar, J. / Schneider, G.
History
DepositionFeb 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2013Provider: 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: UDP-N-acetylenolpyruvoylglucosamine reductase
B: UDP-N-acetylenolpyruvoylglucosamine reductase
C: UDP-N-acetylenolpyruvoylglucosamine reductase
D: UDP-N-acetylenolpyruvoylglucosamine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,46520
Polymers151,0644
Non-polymers7,40216
Water6,125340
1
A: UDP-N-acetylenolpyruvoylglucosamine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6165
Polymers37,7661
Non-polymers1,8504
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: UDP-N-acetylenolpyruvoylglucosamine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6165
Polymers37,7661
Non-polymers1,8504
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: UDP-N-acetylenolpyruvoylglucosamine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6165
Polymers37,7661
Non-polymers1,8504
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: UDP-N-acetylenolpyruvoylglucosamine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6165
Polymers37,7661
Non-polymers1,8504
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)153.700, 154.350, 64.470
Angle α, β, γ (deg.)90.000, 102.260, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-537-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: _ / Auth seq-ID: 2 - 339 / Label seq-ID: 3 - 340

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
UDP-N-acetylenolpyruvoylglucosamine reductase / UDP-N-acetylmuramate dehydrogenase


Mass: 37765.938 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: murB, PA2977 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9HZM7, EC: 1.1.1.158

-
Non-polymers , 5 types, 356 molecules

#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical
ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 2.47 Å3/Da / Density % sol: 50.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M bis-tris propane pH 7.0, 0.2 M sodium potassium tartrate, 15% w/v PEG 3350, 2 mM NADPH, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9762 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 29, 2012 / Details: Toroidal mirror
RadiationMonochromator: Double crystal, Si(111) or Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.23→107.643 Å / Num. all: 69794 / Num. obs: 69794 / % possible obs: 98.2 % / Observed criterion σ(F): 0.8 / Observed criterion σ(I): 0.8 / Redundancy: 3 % / Rsym value: 0.215 / Net I/σ(I): 3.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.23-2.352.60.6860.82606398620.68695.7
2.35-2.530.5881.22898896940.58898.7
2.5-2.6730.4261.62694990480.42698.4
2.67-2.8830.3251.72524884350.32598.1
2.88-3.1630.2193.12339177550.21998.5
3.16-3.533.10.1723.52214271360.17299.4
3.53-4.083.10.1562.71952762830.15699.3
4.08-4.993.10.14241611352620.14298.5
4.99-7.062.80.1473.51123140400.14797.6
7.06-54.2723.40.143.5768422790.1499.1

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
PROCESSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2MBR

2mbr


Resolution: 2.23→54.33 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.895 / WRfactor Rfree: 0.2684 / WRfactor Rwork: 0.2331 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8181 / SU B: 14.963 / SU ML: 0.205 / SU R Cruickshank DPI: 0.378 / SU Rfree: 0.2444 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.378 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2578 3529 5.1 %RANDOM
Rwork0.2225 ---
all0.2243 69784 --
obs0.2243 69784 98.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 264.57 Å2 / Biso mean: 33.0587 Å2 / Biso min: 5.15 Å2
Baniso -1Baniso -2Baniso -3
1--1.68 Å2-0 Å20.51 Å2
2---1.34 Å2-0 Å2
3---2.65 Å2
Refinement stepCycle: LAST / Resolution: 2.23→54.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10580 0 484 340 11404
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01911280
X-RAY DIFFRACTIONr_bond_other_d0.0050.0210812
X-RAY DIFFRACTIONr_angle_refined_deg1.72.02515340
X-RAY DIFFRACTIONr_angle_other_deg0.93324684
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.88751348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.97922.426544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.54151820
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.29115152
X-RAY DIFFRACTIONr_chiral_restr0.0860.21664
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02112660
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022692
X-RAY DIFFRACTIONr_mcbond_it1.4731.9875404
X-RAY DIFFRACTIONr_mcbond_other1.4731.9875403
X-RAY DIFFRACTIONr_mcangle_it2.4492.9786748
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.01 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A22087
12B22087
21A22070
22C22070
31A22084
32D22084
41B22072
42C22072
51B22076
52D22076
61C22070
62D22070
LS refinement shellResolution: 2.232→2.29 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 258 -
Rwork0.348 4602 -
all-4860 -
obs--92.96 %
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)
11.162-0.1702-0.00381.9224-0.41260.8116-0.0475-0.10080.12490.21570.0095-0.0749-0.08830.01410.0380.087-0.0124-0.02320.065-0.0060.017956.49549.130314.7719
21.8318-0.5616-0.29861.1023-0.12570.84260.0057-0.0793-0.1232-0.00240.00170.16450.0795-0.0373-0.00740.0508-0.0301-0.02720.02220.01140.110742.2982-9.503515.2342
32.37370.15890.19541.3054-0.25410.76280.0079-0.21180.07920.09170.00120.1067-0.0267-0.0731-0.00920.04030.01750.00480.0684-0.03630.046-1.6099-12.872114.5078
41.29350.60080.06482.2286-0.40260.994-0.0185-0.0543-0.13340.14730.0437-0.25730.00210.046-0.02530.02510.0309-0.04490.0654-0.04240.151816.9098-27.232815.1393
52.43870.1216-0.39361.40980.09861.1459-0.0578-0.2653-0.07450.13790.0085-0.18580.07350.1570.04930.07120.04180.00070.10450.02730.03411.644127.829614.4974
60.92460.6303-0.21013.02290.31261.2342-0.03760.00510.17630.18220.10880.3804-0.0546-0.0785-0.07120.04260.0480.02760.07780.04920.1811-16.854342.250815.2447
71.08480.20980.22162.137-0.02480.97010.0250.1199-0.0753-0.1722-0.0329-0.02490.07460.03180.00790.08910.03980.01390.06750.00540.009756.69485.9834-14.3026
82.39680.46140.48611.3581-0.010.82740.06110.14910.1675-0.0572-0.02280.1237-0.0620.0122-0.03820.05180.03830.0120.0350.01630.072942.386324.5805-15.0229
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 189
2X-RAY DIFFRACTION2A190 - 339
3X-RAY DIFFRACTION3B2 - 189
4X-RAY DIFFRACTION4B190 - 339
5X-RAY DIFFRACTION5C2 - 189
6X-RAY DIFFRACTION6C190 - 339
7X-RAY DIFFRACTION7D2 - 189
8X-RAY DIFFRACTION8D190 - 339

+
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