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- PDB-5kil: CmlA beta-hydroxylase E377D mutant -

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Basic information

Entry
Database: PDB / ID: 5kil
TitleCmlA beta-hydroxylase E377D mutant
ComponentsCmlA protein
KeywordsOXIDOREDUCTASE / Oxygen activation / Diiron cluster / Antibiotic biosynthesis / Beta-hydroxylase
Function / homology
Function and homology information


4-amino-L-phenylalanyl-[CmlP-peptidyl-carrier-protein] 3-hydroxylase / antibiotic biosynthetic process / oxidoreductase activity / metal ion binding / cytoplasm
Similarity search - Function
Diiron non-heme beta-hydroxylase, N-terminal domain / Diiron non-heme beta-hydroxylase N-terminal domain / Beta-lactamase superfamily domain / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
ACETATE ION / MU-OXO-DIIRON / : / 4-amino-L-phenylalanyl-[CmlP-peptidyl-carrier-protein] 3-hydroxylase
Similarity search - Component
Biological speciesStreptomyces venezuelae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.72 Å
AuthorsKnoot, C.J. / Lipscomb, J.D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM100943 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118030 United States
CitationJournal: Biochemistry / Year: 2016
Title: A Carboxylate Shift Regulates Dioxygen Activation by the Diiron Nonheme beta-Hydroxylase CmlA upon Binding of a Substrate-Loaded Nonribosomal Peptide Synthetase.
Authors: Jasniewski, A.J. / Knoot, C.J. / Lipscomb, J.D. / Que, L.
History
DepositionJun 16, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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

Downloads & links

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Assembly

Deposited unit
A: CmlA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4894
Polymers62,2631
Non-polymers2263
Water34219
1
A: CmlA protein
hetero molecules

A: CmlA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,9778
Polymers124,5262
Non-polymers4526
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area7250 Å2
ΔGint-57 kcal/mol
Surface area37710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.954, 153.954, 92.548
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein CmlA protein


Mass: 62262.875 Da / Num. of mol.: 1 / Mutation: E377D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces venezuelae (strain ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745) (bacteria)
Strain: ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745
Gene: SVEN_0921 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: F2RB80
#2: Chemical ChemComp-FEO / MU-OXO-DIIRON


Mass: 127.689 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2O
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsthe conflict at position 190 is likely due to an error in the genome sequence of the SVEN_0921 gene ...the conflict at position 190 is likely due to an error in the genome sequence of the SVEN_0921 gene from streptomyces venezuelae

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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: 4.57 Å3/Da / Density % sol: 73 % / Description: square bipyramidal
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 20000, potassium acetate, HEPES, glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 11, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.72→38.5 Å / Num. obs: 30307 / % possible obs: 99.8 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 29
Reflection shellResolution: 2.72→2.77 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 4.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.7.0029phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4JO0

4jo0


Resolution: 2.72→38.49 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.917 / SU B: 12.057 / SU ML: 0.229 / Cross valid method: THROUGHOUT / ESU R: 0.327 / ESU R Free: 0.276
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1536 5.1 %RANDOM
Rwork0.202 ---
obs0.205 28730 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 63.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20 Å2
2---0.18 Å20 Å2
3---0.36 Å2
Refinement stepCycle: LAST / Resolution: 2.72→38.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4096 0 8 19 4123
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0194221
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9691.9545742
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4185509
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.45122.146219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.37215659
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8861551
X-RAY DIFFRACTIONr_chiral_restr0.1250.2616
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213327
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.72→2.79 Å
Num. reflection% reflection
Rfree92 -
Rwork2080 -
obs-99.95 %

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