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- PDB-3ht2: Zink containing polyketide cyclase RemF from Streptomyces resisto... -

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Basic information

Entry
Database: PDB / ID: 3ht2
TitleZink containing 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
Cupin 2 conserved barrel domain protein
Similarity search - Component
Biological speciesStreptomyces resistomycificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 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 / Item: _software.name
Revision 1.3Apr 3, 2024Group: 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 / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RemF protein
C: RemF protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2734
Polymers33,1422
Non-polymers1312
Water4,630257
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-91 kcal/mol
Surface area13330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.433, 97.255, 47.743
Angle α, β, γ (deg.)90.00, 91.99, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22C

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERGLUGLU2AA-1 - 1411 - 143
21SERSERGLUGLU2CB-1 - 1411 - 143
12ZNZNZNZN4AC150
22ZNZNZNZN4CD150

NCS ensembles :
ID
1
2

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Components

#1: Protein RemF protein / polyketide cyclase RemF


Mass: 16571.010 Da / Num. of mol.: 2
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.41 Å3/Da / Density % sol: 48.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1M tri-sodium citrate, 0.1M sodium cacodylate, 0.2M ZnCl2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 1.282 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 14, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282 Å / Relative weight: 1
ReflectionResolution: 2→48.62 Å / Num. all: 20594 / Num. obs: 20594 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 23.4
Reflection shellResolution: 2→2.11 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.144 / Mean I/σ(I) obs: 8.6 / Num. unique all: 2495 / % possible all: 82

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Processing

Software
NameVersionClassification
ProDCdata collection
SOLVEphasing
REFMAC5.5.0044refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD
Starting model: Native RemF

Resolution: 2→48.62 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.887 / SU B: 4.384 / SU ML: 0.125 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.207 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2444 1062 5.2 %RANDOM
Rwork0.19314 ---
all0.19577 19508 --
obs0.19577 19508 96.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.966 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å20 Å20.08 Å2
2---1.61 Å20 Å2
3---2.23 Å2
Refinement stepCycle: LAST / Resolution: 2→48.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2272 0 2 257 2531
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222340
X-RAY DIFFRACTIONr_bond_other_d0.0010.021634
X-RAY DIFFRACTIONr_angle_refined_deg1.3391.9743186
X-RAY DIFFRACTIONr_angle_other_deg0.8333968
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1965284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.0223.333114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.89515372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2231520
X-RAY DIFFRACTIONr_chiral_restr0.0760.2338
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212612
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02470
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5741.51436
X-RAY DIFFRACTIONr_mcbond_other0.141.5564
X-RAY DIFFRACTIONr_mcangle_it1.01122352
X-RAY DIFFRACTIONr_scbond_it1.4373904
X-RAY DIFFRACTIONr_scangle_it2.4254.5834
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1830TIGHT POSITIONAL0.110.05
11124MEDIUM POSITIONAL0.190.5
1830TIGHT THERMAL0.280.5
11124MEDIUM THERMAL0.322
21MEDIUM POSITIONAL0.5
21MEDIUM THERMAL0.522
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.213 55 -
Rwork0.18 1123 -
obs--75.85 %

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