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- PDB-4jo0: Crystal Structure of CmlA, a diiron beta-hydroxylase from Strepto... -

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Basic information

Entry
Database: PDB / ID: 4jo0
TitleCrystal Structure of CmlA, a diiron beta-hydroxylase from Streptomyces venezuelae
ComponentsCmlA
KeywordsOXIDOREDUCTASE / nonheme oxygenase / dinuclear iron cluster / antibiotic / beta-hydroxylation
Function / homology
Function and homology information


4-amino-L-phenylalanyl-[CmlP-peptidyl-carrier-protein] 3-hydroxylase / antibiotic biosynthetic process / oxidoreductase activity / metal ion binding
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 / : / : / OXYGEN ATOM / 4-amino-L-phenylalanyl-[CmlP-peptidyl-carrier-protein] 3-hydroxylase
Similarity search - Component
Biological speciesStreptomyces venezuelae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.17 Å
AuthorsKnoot, C.J. / Makris, T.M. / Wilmot, C.M. / Lipscomb, J.D.
CitationJournal: Biochemistry / Year: 2013
Title: Structure of a Dinuclear Iron Cluster-Containing beta-Hydroxylase Active in Antibiotic Biosynthesis.
Authors: Makris, T.M. / Knoot, C.J. / Wilmot, C.M. / Lipscomb, J.D.
History
DepositionMar 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 28, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_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: CmlA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9189
Polymers60,4691
Non-polymers4498
Water2,738152
1
A: CmlA
hetero molecules

A: CmlA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,83618
Polymers120,9382
Non-polymers89816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area8550 Å2
ΔGint-53 kcal/mol
Surface area37990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.158, 153.158, 93.356
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-850-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein CmlA


Mass: 60468.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces venezuelae (bacteria) / Gene: CMLA, SVEN_0921 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: F2RB80, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen

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Non-polymers , 6 types, 160 molecules

#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-O / OXYGEN ATOM / Oxygen


Mass: 15.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 4.53 Å3/Da / Density % sol: 72.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES, 10% PEG20000, 10% glycerol, 100 mM potassium acetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97857 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 27, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionRedundancy: 7.2 % / Av σ(I) over netI: 27.74 / Number: 248828 / Rmerge(I) obs: 0.105 / Χ2: 1.75 / D res high: 2.6 Å / D res low: 21 Å / Num. obs: 34510 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.972199.610.0663.9126.7
5.576.9710010.0742.7847.1
4.885.5710010.0772.5617.2
4.434.8899.910.0752.5136.9
4.124.4310010.0832.4527
3.884.1210010.0942.337.1
3.693.8810010.1082.2967.2
3.533.6999.910.1182.0957.2
3.393.5310010.1272.0377.2
3.273.3910010.1381.6747.2
3.173.2710010.1481.527.3
3.083.1710010.1631.3117.3
33.0810010.1871.1547.3
2.93310010.2041.0747.3
2.862.9310010.2251.0227.4
2.82.8610010.2550.9477.3
2.742.810010.3050.8967.3
2.692.7410010.3360.8657.4
2.642.6910010.3720.8327.4
2.62.6410010.4260.8487.4
ReflectionResolution: 2.17→50 Å / Num. all: 59163 / Num. obs: 57023 / % possible obs: 96.4 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 / Redundancy: 7.3 % / Biso Wilson estimate: 35.1 Å2 / Rmerge(I) obs: 0.063 / Χ2: 0.799 / Net I/σ(I): 7.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.17-2.217.10.43523570.682181.6
2.21-2.257.10.41724510.679184
2.25-2.297.20.38425450.671187.3
2.29-2.347.20.33126310.686190.4
2.34-2.397.20.29527310.69193.3
2.39-2.447.30.26828000.704196.5
2.44-2.517.40.25428820.719198.6
2.51-2.577.40.23229220.724199.9
2.57-2.657.40.19229410.7311100
2.65-2.737.40.16329090.7131100
2.73-2.837.40.13529520.7431100
2.83-2.957.40.10729390.7431100
2.95-3.087.40.0929340.7541100
3.08-3.247.40.07129480.793199.9
3.24-3.447.30.06329670.927199.9
3.44-3.717.30.0629591.146199.8
3.71-4.087.20.05429911.314199.6
4.08-4.677.20.04329771.129199.4
4.67-5.8970.03330360.694199.2
5.89-506.90.02531510.631197.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
SBC-Collectserverdata collection
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.17→38.66 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.2114 / WRfactor Rwork: 0.1839 / Occupancy max: 1 / Occupancy min: 0.24 / FOM work R set: 0.7866 / SU B: 5.383 / SU ML: 0.126 / SU R Cruickshank DPI: 0.157 / SU Rfree: 0.1494 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.157 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2333 2875 5 %RANDOM
Rwork0.201 ---
obs0.2026 54095 96.4 %-
all-56988 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 153.09 Å2 / Biso mean: 53.5916 Å2 / Biso min: 2.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20 Å20 Å2
2--0.68 Å20 Å2
3----1.36 Å2
Refinement stepCycle: LAST / Resolution: 2.17→38.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4195 0 21 152 4368
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0194398
X-RAY DIFFRACTIONr_bond_other_d0.0060.024084
X-RAY DIFFRACTIONr_angle_refined_deg1.7771.9545990
X-RAY DIFFRACTIONr_angle_other_deg1.10639352
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1055536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.68122.338231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.24215689
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6521552
X-RAY DIFFRACTIONr_chiral_restr0.1030.2638
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215052
X-RAY DIFFRACTIONr_gen_planes_other0.0110.021092
LS refinement shellResolution: 2.17→2.226 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 150 -
Rwork0.38 3353 -
all-3503 -
obs--81.83 %

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