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- PDB-1q6w: X-Ray structure of Monoamine oxidase regulatory protein from Arch... -

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Basic information

Entry
Database: PDB / ID: 1q6w
TitleX-Ray structure of Monoamine oxidase regulatory protein from Archaeoglobus fulgius
Componentsmonoamine oxidase regulatory protein, putative
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / NYSGXRC T805 / Hot dog fold / originally observed for the beta-hydroxydecanoyl thiol ester dehydrase / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Function / homologyMaoC-like dehydratase domain / MaoC like domain / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta / Monoamine oxidase regulatory protein, putative
Function and homology information
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.81 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Thirumuruhan, R. / Almo, S.C. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: X-ray structure of monoamine oxidase regulatory protein from Archaeoglobus fulgidus
Authors: Fedorov, A.A. / Fedorov, E.V. / Thirumuruhan, R. / Almo, S.C.
History
DepositionAug 14, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: monoamine oxidase regulatory protein, putative
B: monoamine oxidase regulatory protein, putative
C: monoamine oxidase regulatory protein, putative
D: monoamine oxidase regulatory protein, putative
E: monoamine oxidase regulatory protein, putative
F: monoamine oxidase regulatory protein, putative
G: monoamine oxidase regulatory protein, putative
H: monoamine oxidase regulatory protein, putative
I: monoamine oxidase regulatory protein, putative
J: monoamine oxidase regulatory protein, putative
K: monoamine oxidase regulatory protein, putative
L: monoamine oxidase regulatory protein, putative


Theoretical massNumber of molelcules
Total (without water)218,39812
Polymers218,39812
Non-polymers00
Water00
1
A: monoamine oxidase regulatory protein, putative
B: monoamine oxidase regulatory protein, putative


Theoretical massNumber of molelcules
Total (without water)36,4002
Polymers36,4002
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-25 kcal/mol
Surface area14650 Å2
MethodPISA
2
C: monoamine oxidase regulatory protein, putative
D: monoamine oxidase regulatory protein, putative


Theoretical massNumber of molelcules
Total (without water)36,4002
Polymers36,4002
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-24 kcal/mol
Surface area14840 Å2
MethodPISA
3
E: monoamine oxidase regulatory protein, putative
F: monoamine oxidase regulatory protein, putative


Theoretical massNumber of molelcules
Total (without water)36,4002
Polymers36,4002
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-24 kcal/mol
Surface area14540 Å2
MethodPISA
4
G: monoamine oxidase regulatory protein, putative
H: monoamine oxidase regulatory protein, putative


Theoretical massNumber of molelcules
Total (without water)36,4002
Polymers36,4002
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-25 kcal/mol
Surface area14250 Å2
MethodPISA
5
I: monoamine oxidase regulatory protein, putative
J: monoamine oxidase regulatory protein, putative


Theoretical massNumber of molelcules
Total (without water)36,4002
Polymers36,4002
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-25 kcal/mol
Surface area14200 Å2
MethodPISA
6
K: monoamine oxidase regulatory protein, putative
L: monoamine oxidase regulatory protein, putative


Theoretical massNumber of molelcules
Total (without water)36,4002
Polymers36,4002
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-24 kcal/mol
Surface area14340 Å2
MethodPISA
7
A: monoamine oxidase regulatory protein, putative
B: monoamine oxidase regulatory protein, putative
C: monoamine oxidase regulatory protein, putative
D: monoamine oxidase regulatory protein, putative
E: monoamine oxidase regulatory protein, putative
F: monoamine oxidase regulatory protein, putative


Theoretical massNumber of molelcules
Total (without water)109,1996
Polymers109,1996
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17730 Å2
ΔGint-112 kcal/mol
Surface area35050 Å2
MethodPISA
8
G: monoamine oxidase regulatory protein, putative
H: monoamine oxidase regulatory protein, putative
I: monoamine oxidase regulatory protein, putative
J: monoamine oxidase regulatory protein, putative
K: monoamine oxidase regulatory protein, putative
L: monoamine oxidase regulatory protein, putative


Theoretical massNumber of molelcules
Total (without water)109,1996
Polymers109,1996
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17150 Å2
ΔGint-110 kcal/mol
Surface area34470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.744, 136.503, 127.426
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly probably is a dimer with two fold axis between monomers

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Components

#1: Protein
monoamine oxidase regulatory protein, putative


Mass: 18199.801 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Production host: Escherichia coli (E. coli) / References: UniProt: O28346

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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: 2.58 Å3/Da / Density % sol: 50.49 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 550,BisTris, calcium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.98, 0.97934, 0.97911, 0.97166
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 24, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.981
20.979341
30.979111
40.971661
ReflectionResolution: 2.81→20 Å / Num. all: 53030 / Num. obs: 53030 / % possible obs: 95.8 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 28.6
Reflection shellResolution: 2.8→2.97 Å / Rmerge(I) obs: 0.173 / Mean I/σ(I) obs: 8.2 / % possible all: 89.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.81→20 Å / Rfactor Rfree error: 0.007 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The 6 biological units AB, CD, EF, GH, IJ and KL can be considered as two almost identical hexamers ABCDEF and GHIJKL. First hexamer ABCDEF is well defined in the electron density map while ...Details: The 6 biological units AB, CD, EF, GH, IJ and KL can be considered as two almost identical hexamers ABCDEF and GHIJKL. First hexamer ABCDEF is well defined in the electron density map while the second hexamer GHIJKL is partially disordered.
RfactorNum. reflection% reflectionSelection details
Rfree0.276 2688 4.9 %RANDOM
Rwork0.242 ---
all0.249 53030 --
obs0.249 53030 95.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.7401 Å2 / ksol: 0.313815 e/Å3
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.81→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14224 0 0 0 14224
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.31
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d0.89
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.81→2.9 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.36 -4.1 %
Rwork0.33 4103 -
obs--81 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

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