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- PDB-3ht1: 1.2A structure of the polyketide cyclase RemF from Streptomyces r... -

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Basic information

Entry
Database: PDB / ID: 3ht1
Title1.2A structure of the polyketide cyclase RemF from Streptomyces resistomycificus
ComponentsRemF protein
KeywordsLYASE / cupin fold / ZN-binding / antibiotic biosynthesis / resistomycin / metalloprotein / cyclase
Function / homology
Function and homology information


kinase activity / phosphorylation / metal ion binding
Similarity search - Function
Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
NICKEL (II) ION / Cupin 2 conserved barrel domain protein
Similarity search - Component
Biological speciesStreptomyces resistomycificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.2 Å
AuthorsSilvennoinen, L. / Sandalova, T. / Schneider, G.
CitationJournal: Febs Lett. / Year: 2009
Title: The polyketide cyclase RemF from Streptomyces resistomycificus contains an unusual octahedral zinc binding site
Authors: Silvennoinen, L. / Sandalova, T. / Schneider, G.
History
DepositionJun 11, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RemF protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4422
Polymers16,3831
Non-polymers591
Water3,747208
1
A: RemF protein
hetero molecules

A: RemF protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8844
Polymers32,7672
Non-polymers1172
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area3840 Å2
ΔGint-41 kcal/mol
Surface area12980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.471, 47.907, 96.946
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221

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Components

#1: Protein RemF protein / polyketide cyclase RemF


Mass: 16383.433 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces resistomycificus (bacteria)
Gene: remF / Plasmid: pRARE2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: Q70DX5
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1M tri-sodium citrate, 0.1M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID14-410.975
SYNCHROTRONESRF BM1620.9787
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDFeb 9, 2008
ADSC QUANTUM 210r2CCDDec 14, 2007
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9751
20.97871
ReflectionResolution: 1.15→47.9 Å / Num. all: 53620 / Num. obs: 53620 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 20.6
Reflection shellResolution: 1.15→1.21 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 5.2 / Num. unique all: 5150 / Rsym value: 0.137 / % possible all: 68

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Processing

Software
NameClassification
ProDCdata collection
SOLVEphasing
SHELXL-97refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.2→40 Å / Num. parameters: 12611 / Num. restraintsaints: 15950 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: The structure was refined also with REFMAC 5.2.0019
RfactorNum. reflection% reflectionSelection details
Rfree0.17 2554 5 %RANDOM
Rwork0.1291 ---
all0.1295 49453 --
obs0.1291 49453 97 %-
Refine analyzeNum. disordered residues: 35 / Occupancy sum hydrogen: 1083 / Occupancy sum non hydrogen: 1345
Refinement stepCycle: LAST / Resolution: 1.2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1181 0 1 209 1391
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d0.036
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0299
X-RAY DIFFRACTIONs_zero_chiral_vol0.089
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.081
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.055
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.054
X-RAY DIFFRACTIONs_approx_iso_adps0.105

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