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- PDB-5t7z: Monoclinic crystal form of the EpoB NRPS cyclization-docking bido... -

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Basic information

Entry
Database: PDB / ID: 5t7z
TitleMonoclinic crystal form of the EpoB NRPS cyclization-docking bidomain from Sorangium cellulosum
ComponentsEpoB
KeywordsBIOSYNTHETIC PROTEIN / epothilone / NRPS / thiazoline / cyclization
Function / homology
Function and homology information


organic substance biosynthetic process / phosphopantetheine binding / oxidoreductase activity
Similarity search - Function
TubC, N-terminal docking domain superfamily / TubC, N-terminal docking domain / TubC N-terminal docking domain / Nitroreductase / Nitroreductase family / Nitroreductase-like / Condensation domain / Condensation domain / Amino acid adenylation domain / AMP-binding, conserved site ...TubC, N-terminal docking domain superfamily / TubC, N-terminal docking domain / TubC N-terminal docking domain / Nitroreductase / Nitroreductase family / Nitroreductase-like / Condensation domain / Condensation domain / Amino acid adenylation domain / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
Similarity search - Domain/homology
Biological speciesSorangium cellulosum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.03 Å
AuthorsDowling, D.P. / Kung, Y. / Croft, A.K. / Taghizadeh, K. / Kelly, W.L. / Walsh, C.T. / Drennan, C.L.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structural elements of an NRPS cyclization domain and its intermodule docking domain.
Authors: Dowling, D.P. / Kung, Y. / Croft, A.K. / Taghizadeh, K. / Kelly, W.L. / Walsh, C.T. / Drennan, C.L.
History
DepositionSep 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EpoB


Theoretical massNumber of molelcules
Total (without water)61,7641
Polymers61,7641
Non-polymers00
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.768, 90.115, 63.337
Angle α, β, γ (deg.)90.000, 102.740, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein EpoB


Mass: 61764.223 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sorangium cellulosum (bacteria) / Gene: epoB / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KIZ9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsNcoI restriction site was used for the original cloning into pET30a, introducing an Ala ...NcoI restriction site was used for the original cloning into pET30a, introducing an Ala substitution for Thr at position two

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.6 % / Description: monoclinic plates
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein at 20 mg mL-1 was incubated with 10 mM acetyl coenzyme A and 30 mM 2-methyl-thiazole-4-carboxylic acid ethyl ester (Synthonix, Wake Forest, NC). Well solution: 56% tacsimate (pH 7.0; ...Details: Protein at 20 mg mL-1 was incubated with 10 mM acetyl coenzyme A and 30 mM 2-methyl-thiazole-4-carboxylic acid ethyl ester (Synthonix, Wake Forest, NC). Well solution: 56% tacsimate (pH 7.0; Hampton Research, Aliso Viejo, CA) and 1% PEG 1,500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97917 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionResolution: 2.03→50 Å / Num. obs: 35020 / % possible obs: 98.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 22.69 Å2 / Rsym value: 0.126 / Net I/σ(I): 8.8
Reflection shellResolution: 2.03→2.1 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 2 / % possible all: 92.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: R32 EpoBcy

Resolution: 2.03→36.404 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2116 1719 4.95 %5%
Rwork0.1805 32990 --
obs0.1821 34709 98.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.64 Å2 / Biso mean: 28.6716 Å2 / Biso min: 10.98 Å2
Refinement stepCycle: final / Resolution: 2.03→36.404 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3964 0 0 287 4251
Biso mean---33.3 -
Num. residues----493
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034129
X-RAY DIFFRACTIONf_angle_d0.6455636
X-RAY DIFFRACTIONf_chiral_restr0.026641
X-RAY DIFFRACTIONf_plane_restr0.003734
X-RAY DIFFRACTIONf_dihedral_angle_d12.5491581
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.03-2.08980.28741460.22912558270492
2.0898-2.15720.26431310.21932700283197
2.1572-2.23430.2281410.19872743288499
2.2343-2.32370.24921410.194227612902100
2.3237-2.42950.2261550.193627842939100
2.4295-2.55750.22371270.202627992926100
2.5575-2.71770.2721360.200227682904100
2.7177-2.92750.221670.19182765293299
2.9275-3.22190.20381520.18582752290499
3.2219-3.68770.19081410.16072775291699
3.6877-4.64460.17571470.15072773292099
4.6446-36.40950.18611350.16782812294798
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)
11.13-0.0821-0.34792.1947-0.18670.9863-0.0310.0107-0.1513-0.0028-0.0263-0.54290.23290.16360.060.2739-0.0208-0.00050.22-0.0160.3417-6.8345-17.275341.1621
21.0372-0.0565-0.17730.35050.10610.86520.01240.1152-0.0017-0.0478-0.03180.0186-0.02960.03230.01410.14510.0141-0.02330.14510.00840.132914.7742.595912.3977
30.91650.20510.25910.78940.43771.16520.029-0.17320.0446-0.0063-0.04930.0463-0.0525-0.08320.01190.17380.00410.03350.16710.00660.164711.33858.30738.7471
40.6959-0.2551-0.35810.68390.35731.4223-0.0493-0.09720.03620.03760.0901-0.044-0.09980.1835-0.03530.2124-0.01320.01820.22460.00040.193423.16558.113133.3687
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 2:59)A2 - 59
2X-RAY DIFFRACTION2(chain A and resid 60:242)A60 - 242
3X-RAY DIFFRACTION3(chain A and resid 243:405)A243 - 405
4X-RAY DIFFRACTION4(chain A and resid 406:497)A406 - 497

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