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- PDB-3gz7: Crystal structure of Putative antibiotic biosynthesis monooxygena... -

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Basic information

Entry
Database: PDB / ID: 3gz7
TitleCrystal structure of Putative antibiotic biosynthesis monooxygenase (NP_888398.1) from BORDETELLA BRONCHISEPTICA at 2.15 A resolution
ComponentsPutative antibiotic biosynthesis monooxygenase
KeywordsBIOSYNTHETIC PROTEIN / NP_888398.1 / Putative antibiotic biosynthesis monooxygenase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Antibiotic biosynthesis monooxygenase / dimeric alpha-beta barrel
Function / homology
Function and homology information


ABM domain profile. / Antibiotic biosynthesis monooxygenase / Antibiotic biosynthesis monooxygenase domain / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / ABM domain-containing protein / ABM domain-containing protein
Similarity search - Component
Biological speciesBordetella bronchiseptica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.15 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative antibiotic biosynthesis monooxygenase (NP_888398.1) from BORDETELLA BRONCHISEPTICA at 2.15 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id ..._pdbx_entry_details.has_protein_modification / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative antibiotic biosynthesis monooxygenase
B: Putative antibiotic biosynthesis monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4684
Polymers27,0832
Non-polymers3842
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-7 kcal/mol
Surface area10020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.692, 55.807, 40.658
Angle α, β, γ (deg.)90.000, 97.280, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-120-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 4 / Auth seq-ID: -1 - 96 / Label seq-ID: 18 - 115

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Putative antibiotic biosynthesis monooxygenase


Mass: 13541.642 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella bronchiseptica (bacteria) / Gene: BB1853, NP_888398.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q7WL96, UniProt: A0A0H3LTZ0*PLUS
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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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: 2.15 Å3/Da / Density % sol: 42.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.64
Details: 27.5000% polyethylene glycol 6000, 0.1M citric acid pH 4.64, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97966,0.97946
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 18, 2009 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979661
30.979461
ReflectionResolution: 2.15→29.21 Å / Num. obs: 12610 / % possible obs: 99.8 % / Redundancy: 3.1 % / Biso Wilson estimate: 20.718 Å2 / Rmerge(I) obs: 0.163 / Rsym value: 0.163 / Net I/σ(I): 4.372
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.15-2.213.10.6191.228329200.61999.9
2.21-2.273.10.5351.428239230.53599.8
2.27-2.333.10.5721.326538580.572100
2.33-2.43.10.4511.726418560.451100
2.4-2.483.10.3941.925758280.39499.8
2.48-2.573.10.3911.924888070.39199.9
2.57-2.673.10.3382.224247780.338100
2.67-2.783.10.243.122697360.24100
2.78-2.93.10.223.422427250.22100
2.9-3.043.10.1963.820696690.19699.8
3.04-3.213.10.147520436610.147100
3.21-3.43.10.118619326290.118100
3.4-3.633.10.0967.117995820.09699.9
3.63-3.933.10.0838.416705390.08399.9
3.93-4.33.10.0689.815464970.06899.7
4.3-4.813.10.06310.113794470.06399.7
4.81-5.553.10.0748.812394020.07499.7
5.55-6.830.08910593480.0899.5
6.8-9.623.10.06111.77962590.06198.6
9.62-29.212.90.05510.74231460.05594.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.15→29.21 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.913 / Occupancy max: 1 / Occupancy min: 0.22 / SU B: 5.315 / SU ML: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.228 / ESU R Free: 0.198
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. CITRATE (CIT) MOLECULES ARE MODELED BASED ON THE CRYSTALLIZATION CONDITION. 4. THERE ARE UNEXPLAINED ELECTRON DENSITIES FOUND NEAR NON-CRYSTALLOGRAPHIC 2-FOLD BETWEEN ILE 5 OF A AND B MOLECULES. THEY ARE NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.236 617 4.9 %RANDOM
Rwork0.174 ---
obs0.177 12610 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 65.44 Å2 / Biso mean: 22.559 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20 Å20.01 Å2
2--1.17 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 2.15→29.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1599 0 26 145 1770
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211665
X-RAY DIFFRACTIONr_bond_other_d0.0010.021135
X-RAY DIFFRACTIONr_angle_refined_deg1.6261.942259
X-RAY DIFFRACTIONr_angle_other_deg1.00832737
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0935201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.26723.21887
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.20615270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.4291516
X-RAY DIFFRACTIONr_chiral_restr0.0970.2232
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021898
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02358
X-RAY DIFFRACTIONr_nbd_refined0.1910.2285
X-RAY DIFFRACTIONr_nbd_other0.1990.21154
X-RAY DIFFRACTIONr_nbtor_refined0.1780.2735
X-RAY DIFFRACTIONr_nbtor_other0.0840.2895
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2104
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2830.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3110.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2830.210
X-RAY DIFFRACTIONr_mcbond_it2.31831114
X-RAY DIFFRACTIONr_mcbond_other0.723400
X-RAY DIFFRACTIONr_mcangle_it3.08451611
X-RAY DIFFRACTIONr_scbond_it5.3818715
X-RAY DIFFRACTIONr_scangle_it6.84911648
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1338 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.330.5
MEDIUM THERMAL1.42
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 39 -
Rwork0.21 879 -
all-918 -
obs--99.89 %

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