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- PDB-4ffu: CRYSTAL STRUCTURE OF putative MaoC-like (monoamine oxidase-like) ... -

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Basic information

Entry
Database: PDB / ID: 4ffu
TitleCRYSTAL STRUCTURE OF putative MaoC-like (monoamine oxidase-like) protein, similar to NodN from Sinorhizo Bium meliloti 1021
Componentsoxidase
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGRC / oxidase / PSI-Biology / New York Structural Genomics Research Consortium
Function / homology
Function and homology information


monoamine oxidase / oxidoreductase activity
Similarity search - Function
MaoC-like dehydratase domain / MaoC like domain / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Putative MaoC-like (Monoamine oxidase-like) protein, similar to NodN
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsMalashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. ...Malashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. / Villegas, G. / Evans, B. / Zenchek, W. / Love, J. / Fiser, A. / Khafizov, K. / Seidel, R. / Bonanno, J.B. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: CRYSTAL STRUCTURE OF putative MaoC-like (monoamine oxidase-like) protein, similar to NodN from Sinorhizo Bium meliloti 1021
Authors: Malashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. ...Authors: Malashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. / Villegas, G. / Evans, B. / Zenchek, W. / Love, J. / Fiser, A. / Khafizov, K. / Seidel, R. / Bonanno, J.B. / Almo, S.C.
History
DepositionJun 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: oxidase
B: oxidase
C: oxidase
D: oxidase
E: oxidase
F: oxidase
G: oxidase
H: oxidase
I: oxidase
J: oxidase
K: oxidase
L: oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)239,96013
Polymers239,92512
Non-polymers351
Water32,9491829
1
A: oxidase
D: oxidase
E: oxidase
F: oxidase
I: oxidase
J: oxidase


Theoretical massNumber of molelcules
Total (without water)119,9626
Polymers119,9626
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15740 Å2
ΔGint-91 kcal/mol
Surface area37050 Å2
MethodPISA
2
B: oxidase
C: oxidase
G: oxidase
H: oxidase
K: oxidase
L: oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,9987
Polymers119,9626
Non-polymers351
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15220 Å2
ΔGint-93 kcal/mol
Surface area36640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.490, 122.938, 147.685
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailshexameric

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Components

#1: Protein
oxidase / / Putative MaoC-like (Monoamine oxidase-like) protein / similar to NodN


Mass: 19993.734 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: RB0689, SM_b21110 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: Q92VL2, monoamine oxidase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1829 / 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: 2.2 Å3/Da / Density % sol: 44.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M LiCl, 0.1M HEPES, 25% PEG 6000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 194995 / % possible obs: 99.8 % / Redundancy: 7 % / Rmerge(I) obs: 0.094 / Χ2: 1.214 / Net I/σ(I): 10.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.836.70.49995181.314198.8
1.83-1.8670.42396991.331100
1.86-1.970.37697001.3351100
1.9-1.947.10.33596711.3641100
1.94-1.987.10.29196621.3421100
1.98-2.037.10.24997111.3461100
2.03-2.087.10.21597261.3291100
2.08-2.137.10.19796641.3241100
2.13-2.27.10.16597061.2751100
2.2-2.277.10.14797531.2341100
2.27-2.357.10.13697121.2411100
2.35-2.447.10.12597041.151199.9
2.44-2.557.10.1197701.173199.9
2.55-2.6970.10197461.164199.9
2.69-2.8670.09297651.121199.9
2.86-3.086.90.08497961.012199.8
3.08-3.396.70.07797671.147199.7
3.39-3.886.60.06598411.097199.5
3.88-4.886.60.05298771.025199.4
4.88-506.70.05102070.946199.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å45.73 Å
Translation2.5 Å45.73 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1Q6W

1q6w


Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.205 / WRfactor Rwork: 0.1726 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.887 / SU B: 4.054 / SU ML: 0.066 / SU R Cruickshank DPI: 0.1125 / SU Rfree: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.1969 9811 5 %RANDOM
Rwork0.1668 ---
obs0.1683 194753 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 114.9 Å2 / Biso mean: 25.3837 Å2 / Biso min: 7.39 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14074 0 1 1829 15904
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01914741
X-RAY DIFFRACTIONr_angle_refined_deg1.3251.94720041
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.81251872
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.52322.085729
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.901152286
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.91515163
X-RAY DIFFRACTIONr_chiral_restr0.0940.22215
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02111486
LS refinement shellResolution: 1.802→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 682 -
Rwork0.231 13398 -
all-14080 -
obs--99.01 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0853-0.2132-0.0440.63570.17620.23880.01660.0218-0.0247-0.031-0.00650.0153-0.0064-0.0021-0.01020.01780.0054-0.020.0301-0.0260.03773.489239.937638.8704
20.1701-0.28980.20261.097-0.5130.2880.00160.05710.0164-0.0276-0.00430.01870.01140.0410.00270.04880.01670.02490.04130.02250.01954.597381.570236.9871
30.72750.02180.04020.2075-0.02880.08090.01290.0145-0.1237-0.0504-0.00770.00730.003-0.0557-0.00520.01330.0055-0.00380.0474-0.01030.032353.719946.297853.1802
40.63960.1632-0.08750.5588-0.09520.2956-0.0099-0.00850.0733-0.0145-0.0119-0.0375-0.03490.07210.02180.0076-0.0111-0.00640.01980.00930.0223.017176.687352.0379
50.1295-0.08390.04480.42660.00120.56640.00080.0361-0.0279-0.07070.0208-0.042-0.06920.1197-0.02170.0241-0.02050.00880.0512-0.00620.024214.610452.197538.0989
60.7298-0.1553-0.08080.6696-0.08020.7631-0.0468-0.1418-0.04850.12330.08540.0764-0.0235-0.0346-0.03860.02770.02430.00960.05310.01370.02-16.24249.088769.2728
70.7855-0.35210.30940.9514-0.19780.7652-0.1011-0.1220.110.19650.0958-0.1857-0.1108-0.01590.00520.05250.0266-0.03020.0341-0.01980.048274.410674.657168.6139
80.2242-0.0673-0.19160.616-0.10030.2243-0.0133-0.0221-0.04860.0943-0.01190.012-0.0198-0.00270.02520.01620.0060.00580.03860.02540.022958.028951.446667.9719
90.15040.11660.07940.68690.05240.22150.0083-0.0430.03290.1396-0.03560.0377-0.02840.01630.02730.0388-0.0057-0.00110.025-0.01180.0127-0.99172.959866.9543
100.4879-0.249-0.10291.336-0.13250.1531-0.0305-0.026-0.14190.03260.02070.19210.0104-0.00140.00980.03330.0045-0.00790.02660.01640.0681-7.379237.105666.9255
110.8987-0.3082-0.01940.92450.06260.22520.0006-0.01060.25010.04580.0057-0.187-0.0819-0.0172-0.00630.07570.00530.00710.0029-0.00430.087764.824186.343365.7129
120.15770.0292-0.03940.4863-0.06180.6319-0.03170.0456-0.0141-0.09620.07780.0280.0297-0.1321-0.04620.046-0.003-0.00770.06410.00510.007343.559570.515237.7044
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-6 - 148
2X-RAY DIFFRACTION2B-1 - 148
3X-RAY DIFFRACTION3C4 - 153
4X-RAY DIFFRACTION4D3 - 149
5X-RAY DIFFRACTION5E3 - 153
6X-RAY DIFFRACTION6F3 - 147
7X-RAY DIFFRACTION7G3 - 147
8X-RAY DIFFRACTION8H-7 - 148
9X-RAY DIFFRACTION9I-7 - 149
10X-RAY DIFFRACTION10J4 - 146
11X-RAY DIFFRACTION11K4 - 146
12X-RAY DIFFRACTION12L3 - 153

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