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- PDB-5xny: Crystal structure of CreD -

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Basic information

Entry
Database: PDB / ID: 5xny
TitleCrystal structure of CreD
ComponentsCreD
KeywordsLYASE / aspartase / fumarase / cremeomycin / nitrous acid
Function / homology
Function and homology information


nitrosuccinate lyase / 3,4-dihydroxybenzoate catabolic process / antibiotic biosynthetic process / lyase activity
Similarity search - Function
3-carboxy-cis,cis-muconate cycloisomerase / Adenylosuccinate lyase C-terminus / Adenylosuccinate lyase C-terminal / Adenylosuccinate lyase C-terminus / Fumarase/aspartase (N-terminal domain) / Fumarase/aspartase (Central domain) / Fumarase C; Chain A, domain 2 / Fumarase C; Chain B, domain 1 / Fumarate lyase family / Fumarate lyase, N-terminal ...3-carboxy-cis,cis-muconate cycloisomerase / Adenylosuccinate lyase C-terminus / Adenylosuccinate lyase C-terminal / Adenylosuccinate lyase C-terminus / Fumarase/aspartase (N-terminal domain) / Fumarase/aspartase (Central domain) / Fumarase C; Chain A, domain 2 / Fumarase C; Chain B, domain 1 / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Fumarase/histidase, N-terminal / L-Aspartase-like / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Nitrosuccinate lyase
Similarity search - Component
Biological speciesStreptomyces cremeus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsKatsuyama, Y. / Sato, Y. / Sugai, Y. / Higashiyama, Y. / Senda, M. / Senda, T. / Ohnishi, Y.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science25850048 Japan
Japan Society for the Promotion of Science16K14908 Japan
Ministry of Education, Culture, Sports, Science and Technology of JapanNC-CARP Japan
Japan Agency for Medical Research and Development Japan
CitationJournal: FEBS J. / Year: 2018
Title: Crystal structure of the nitrosuccinate lyase CreD in complex with fumarate provides insights into the catalytic mechanism for nitrous acid elimination
Authors: Katsuyama, Y. / Sato, Y. / Sugai, Y. / Higashiyama, Y. / Senda, M. / Senda, T. / Ohnishi, Y.
History
DepositionMay 25, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2018Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year
Revision 1.2May 2, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CreD


Theoretical massNumber of molelcules
Total (without water)50,8051
Polymers50,8051
Non-polymers00
Water1,964109
1
A: CreD

A: CreD

A: CreD

A: CreD


Theoretical massNumber of molelcules
Total (without water)203,2204
Polymers203,2204
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_657-x+1,y,-z+21
crystal symmetry operation4_567x,-y+1,-z+21
Buried area26210 Å2
ΔGint-184 kcal/mol
Surface area51970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.810, 98.220, 124.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein CreD


Mass: 50804.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces cremeus (bacteria) / Gene: creD / Plasmid: pColdI / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0K2JL82
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.97 %
Description: the entry contains Friedel pairs in F_Plus/Minus columns
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 0.1 M Tris-HCl, pH 8.2-8.5 containing 1.8-2.0 M ammonium sulfate

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 17, 2016
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.18→19.918 Å / Num. obs: 47180 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 4.416 % / Biso Wilson estimate: 32.68 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.084 / Χ2: 0.994 / Net I/σ(I): 13.63
Reflection shellResolution: 2.18→2.24 Å / Redundancy: 3.163 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.45 / Num. unique obs: 3342 / CC1/2: 0.903 / Rrim(I) all: 0.586 / % possible all: 94.6

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RE5

1re5


Resolution: 2.18→19.918 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.56 / Stereochemistry target values: ML
Details: the entry contains Friedel pairs in F_Plus/Minus columns
RfactorNum. reflection% reflectionSelection details
Rfree0.2147 2370 5.03 %Random selection
Rwork0.1834 ---
obs0.1851 47156 99.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.18→19.918 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3045 0 0 109 3154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073085
X-RAY DIFFRACTIONf_angle_d0.8094218
X-RAY DIFFRACTIONf_dihedral_angle_d2.6051850
X-RAY DIFFRACTIONf_chiral_restr0.043526
X-RAY DIFFRACTIONf_plane_restr0.006552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.22450.30761350.29832537X-RAY DIFFRACTION94
2.2245-2.27280.38081320.25972551X-RAY DIFFRACTION97
2.2728-2.32560.25531410.22562664X-RAY DIFFRACTION100
2.3256-2.38360.27011420.21312644X-RAY DIFFRACTION100
2.3836-2.4480.2171450.20172668X-RAY DIFFRACTION100
2.448-2.51990.26931370.20512620X-RAY DIFFRACTION100
2.5199-2.60110.26321400.20672645X-RAY DIFFRACTION100
2.6011-2.69380.251410.20762632X-RAY DIFFRACTION100
2.6938-2.80140.25521400.19682630X-RAY DIFFRACTION100
2.8014-2.92850.21261440.19192671X-RAY DIFFRACTION100
2.9285-3.08240.24091360.19752626X-RAY DIFFRACTION100
3.0824-3.27470.22991420.19912670X-RAY DIFFRACTION100
3.2747-3.52620.19761400.17682644X-RAY DIFFRACTION100
3.5262-3.87870.20231390.16622633X-RAY DIFFRACTION100
3.8787-4.43460.13851410.14442651X-RAY DIFFRACTION100
4.4346-5.56690.19311360.16222646X-RAY DIFFRACTION100
5.5669-19.91870.20141390.16592654X-RAY DIFFRACTION100

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