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- PDB-3d1c: Crystal structure of Flavin-containing Putative Monooxygenase (NP... -

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Basic information

Entry
Database: PDB / ID: 3d1c
TitleCrystal structure of Flavin-containing Putative Monooxygenase (NP_373108.1) from STAPHYLOCOCCUS AUREUS MU50 at 2.40 A resolution
ComponentsFlavin-containing Putative Monooxygenase
KeywordsOXIDOREDUCTASE / NP_373108.1 / Flavin-containing Putative Monooxygenase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Pyridine nucleotide-disulphide oxidoreductase
Function / homology
Function and homology information


Oxidoreductases / monooxygenase activity / flavin adenine dinucleotide binding
Similarity search - Function
: / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Unknown ligand / NAD(P)-binding domain-containing protein / Putative flavoprotein monooxygenase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2014
Title: Crystal structure of a Baeyer-Villiger flavin-containing monooxygenase from Staphylococcus aureus MRSA strain MU50.
Authors: Hwang, W.C. / Xu, Q. / Wu, B. / Godzik, A.
History
DepositionMay 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 20, 2014Group: Database references
Revision 1.3Dec 23, 2015Group: Database references
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.5Jul 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 1.6Feb 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 1.7Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flavin-containing Putative Monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8107
Polymers41,6401
Non-polymers1,1706
Water2,072115
1
A: Flavin-containing Putative Monooxygenase
hetero molecules

A: Flavin-containing Putative Monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,62014
Polymers83,2802
Non-polymers2,34012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area9380 Å2
ΔGint-178 kcal/mol
Surface area28630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.247, 109.247, 87.061
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-372-

SO4

DetailsAUTHOR STATE THAT ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein Flavin-containing Putative Monooxygenase


Mass: 41640.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Mu50 / Gene: NP_373108.1, SAV2584 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q99R54, UniProt: A0A0H3JN45*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 3.12 Å3/Da / Density % sol: 60.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 1.6000M (NH4)2SO4, 0.1M MES pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97920,0.91837
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 4, 2008 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.918371
ReflectionResolution: 2.4→28.892 Å / Num. obs: 21169 / % possible obs: 99.9 % / Redundancy: 4.8 % / Biso Wilson estimate: 49.14 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 7.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.4-2.464.90.6821.1733815120.682100
2.46-2.534.80.5751.3729915070.575100
2.53-2.64.80.4811.6701114460.481100
2.6-2.684.90.3932693514290.393100
2.68-2.774.80.3112.4662813700.311100
2.77-2.874.80.2563649513420.256100
2.87-2.984.80.2113.6623312910.211100
2.98-3.14.80.1594.7599212420.159100
3.1-3.244.80.1285.8569711840.128100
3.24-3.394.80.0957.7552111460.095100
3.39-3.584.80.0789525410970.078100
3.58-3.794.70.0729.1494410420.072100
3.79-4.064.70.0689.546639820.068100
4.06-4.384.70.06210.243379180.062100
4.38-4.84.70.0511240248520.051100
4.8-5.374.70.04613.836147690.046100
5.37-6.24.60.0513.731926930.05100
6.2-7.594.50.05312.326785900.05399.9
7.59-10.734.40.0416.320974820.0499.9
10.73-28.893.90.03816.610762750.03895.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3.004data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→28.892 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / SU B: 12.376 / SU ML: 0.148 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.266 / ESU R Free: 0.212
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. 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. 4. FAD IS MODELED BASED ON DENSITY AND STRUCTURAL HOMOLOGY. SO4 IS PRESENT IN CRYSTALLIZATION CONDITION. AN UNKNOWN LIGAND (UNL) WAS MODELLED AT THE PUTATIVE ACTIVE SITE BASED ON A STRUCTURAL HOMOLOG (PDB 2GVC). 5. DENSITY FOR THE FOLLOWING REGIONS ARE POOR: A62,A118,
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1087 5.1 %RANDOM
Rwork0.181 ---
obs0.183 21137 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.373 Å2
Baniso -1Baniso -2Baniso -3
1--1.52 Å20 Å20 Å2
2---1.52 Å20 Å2
3---3.05 Å2
Refinement stepCycle: LAST / Resolution: 2.4→28.892 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2773 0 84 115 2972
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222916
X-RAY DIFFRACTIONr_bond_other_d0.0010.021814
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.9573983
X-RAY DIFFRACTIONr_angle_other_deg0.93434437
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.825356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.26724.741135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.12115424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.972157
X-RAY DIFFRACTIONr_chiral_restr0.0860.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023262
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02593
X-RAY DIFFRACTIONr_nbd_refined0.1980.2537
X-RAY DIFFRACTIONr_nbd_other0.1930.21781
X-RAY DIFFRACTIONr_nbtor_refined0.1860.21405
X-RAY DIFFRACTIONr_nbtor_other0.0850.21434
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2110.2138
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1470.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2360.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.28
X-RAY DIFFRACTIONr_mcbond_it2.08531838
X-RAY DIFFRACTIONr_mcbond_other0.4213726
X-RAY DIFFRACTIONr_mcangle_it3.35152862
X-RAY DIFFRACTIONr_scbond_it4.95981287
X-RAY DIFFRACTIONr_scangle_it6.369111121
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 88 -
Rwork0.252 1420 -
all-1508 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 35.2065 Å / Origin y: 28.2679 Å / Origin z: 25.7464 Å
111213212223313233
T-0.085 Å2-0.0025 Å20.0022 Å2--0.1121 Å20.0053 Å2---0.0777 Å2
L0.7248 °20.4477 °2-0.2669 °2-2.6499 °20.1441 °2--1.1768 °2
S0.002 Å °0.1261 Å °0.0451 Å °-0.2706 Å °0.0548 Å °0.0213 Å °0.0216 Å °-0.1469 Å °-0.0568 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 3682 - 369
2X-RAY DIFFRACTION1AF5001

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