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- PDB-1tz0: Crystal Structure of Putative Antibiotic Biosythesis Monooxygenas... -

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Basic information

Entry
Database: PDB / ID: 1tz0
TitleCrystal Structure of Putative Antibiotic Biosythesis Monooxygenase from Bacillus cereus
Componentshypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Protein Structure Initiative / MCSG / Hypothetical Protein / Bacillus cereus / PSI / Midwest Center for Structural Genomics
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
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
FORMIC ACID / ABM domain-containing protein
Similarity search - Component
Biological speciesBacillus cereus ATCC 14579 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.84 Å
AuthorsKim, Y. / Lezondra, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Hypothetical Protein APC24875 from Bacillus cereus
Authors: Kim, Y. / Lezondra, L. / Joachimiak, A.
History
DepositionJul 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Remark 300BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). THE AUTHORS STATE THAT THE BIOLOGICAL ASSEMBLY IS NOT NECESSARILY THE CONTENT OF THE ASYMMETRIC UNIT. THEY FOUND THAT OTHER STRUCTURES, HOMOLOGOUS TO THIS STRUCTURE FORM DIMERS. THIS STRUCTURE FORMS A SIMILAR DIMER AS WELL AS AN ASYMMETRIC TRIMER WHICH SEEMS INTIMATE ENOUGH. FOR THESE REASONS AUTHORS STATE STRUCTURE AS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein
B: hypothetical protein
C: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5995
Polymers39,4913
Non-polymers1082
Water7,512417
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)123.894, 86.080, 42.867
Angle α, β, γ (deg.)90.00, 90.10, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-592-

HOH

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Components

#1: Protein hypothetical protein /


Mass: 13163.535 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus ATCC 14579 (bacteria) / Species: Bacillus cereus / Strain: ATCC 14579 / DSM 31 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q81C15
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 417 / 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: 3.1 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: Sodium Formate, Sodium Acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793, 0.9794, 0.954
DetectorType: SBC-2 / Detector: CCD / Date: Mar 20, 2004 / Details: mirrors
RadiationMonochromator: double crystal monochromator Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97941
30.9541
ReflectionResolution: 1.84→40 Å / Num. all: 40217 / Num. obs: 38958 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 9.3
Reflection shellResolution: 1.84→1.91 Å / Redundancy: 5 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 2.3 / Num. unique all: 3690 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
SBC-Collectdata collection
CrystalClearD*TRECK (MSC/RIGAKU)data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.84→37.27 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.911 / SU B: 3.152 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26073 3841 10 %RANDOM
Rwork0.20398 ---
all0.2096 34428 --
obs0.20962 34428 98.23 %-
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: 25.499 Å2
Baniso -1Baniso -2Baniso -3
1--0.91 Å20 Å2-0.43 Å2
2--1.42 Å20 Å2
3----0.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.145 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.84→37.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2498 0 7 417 2922
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212558
X-RAY DIFFRACTIONr_bond_other_d0.0020.022283
X-RAY DIFFRACTIONr_angle_refined_deg1.3331.9233440
X-RAY DIFFRACTIONr_angle_other_deg0.77335319
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4445301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0870.2371
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022792
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02537
X-RAY DIFFRACTIONr_nbd_refined0.2240.2494
X-RAY DIFFRACTIONr_nbd_other0.2530.22546
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0830.21544
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2262
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3110.2151
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.243
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.9491.51511
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.72322445
X-RAY DIFFRACTIONr_scbond_it2.25931047
X-RAY DIFFRACTIONr_scangle_it3.6974.5995
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.836→1.884 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.349 238
Rwork0.303 2063
obs-2063

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