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- PDB-1qaf: THE ACTIVE SITE BASE CONTROLS COFACTOR REACTIVITY IN ESCHERICHIA ... -

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Basic information

Entry
Database: PDB / ID: 1qaf
TitleTHE ACTIVE SITE BASE CONTROLS COFACTOR REACTIVITY IN ESCHERICHIA COLI AMINE OXIDASE : X-RAY CRYSTALLOGRAPHIC STUDIES WITH MUTATIONAL VARIANTS
ComponentsPROTEIN (COPPER AMINE OXIDASE)
KeywordsOXIDOREDUCTASE / CATALYTIC DOMAIN MAINLY ANTI-PARALLEL BETA SHEET / THREE PERIPHERAL ALPHA-BETA DOMAINS
Function / homology
Function and homology information


phenylethylamine catabolic process / primary-amine oxidase / aliphatic amine oxidase activity / primary methylamine oxidase activity / L-phenylalanine catabolic process / amine metabolic process / quinone binding / periplasmic space / copper ion binding / calcium ion binding
Similarity search - Function
Copper amine oxidase-like, N-terminal domain / Copper amine oxidase-like, N-terminal / Copper amine oxidase-like, N-terminal domain superfamily / Copper amine oxidase N-terminal domain / Copper Amine Oxidase; Chain A, domain 1 / Copper amine oxidase, N3-terminal / Copper amine oxidase, N2-terminal / Copper amine oxidase, N2 domain / Copper amine oxidase, N3 domain / Copper amine oxidase, catalytic domain ...Copper amine oxidase-like, N-terminal domain / Copper amine oxidase-like, N-terminal / Copper amine oxidase-like, N-terminal domain superfamily / Copper amine oxidase N-terminal domain / Copper Amine Oxidase; Chain A, domain 1 / Copper amine oxidase, N3-terminal / Copper amine oxidase, N2-terminal / Copper amine oxidase, N2 domain / Copper amine oxidase, N3 domain / Copper amine oxidase, catalytic domain / Copper amine oxidase copper-binding site signature. / Copper amine oxidase topaquinone signature. / Nuclear Transport Factor 2; Chain: A, - #40 / Copper amine oxidase / Copper amine oxidase, catalytic domain / Copper amine oxidase, N-terminal / Copper amine oxidase, catalytic domain superfamily / Copper amine oxidase, enzyme domain / Beta-galactosidase; Chain A, domain 5 / Nuclear Transport Factor 2; Chain: A, / Distorted Sandwich / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
COPPER (II) ION / Primary amine oxidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER / Resolution: 2.2 Å
AuthorsMurray, J.M. / Wilmot, C.M. / Saysell, C.G. / Jaeger, J. / Knowles, P.F. / Phillips, S.E. / McPherson, M.J.
CitationJournal: Biochemistry / Year: 1999
Title: The active site base controls cofactor reactivity in Escherichia coli amine oxidase: x-ray crystallographic studies with mutational variants.
Authors: Murray, J.M. / Saysell, C.G. / Wilmot, C.M. / Tambyrajah, W.S. / Jaeger, J. / Knowles, P.F. / Phillips, S.E. / McPherson, M.J.
History
DepositionMar 11, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (COPPER AMINE OXIDASE)
B: PROTEIN (COPPER AMINE OXIDASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,9789
Polymers161,5982
Non-polymers3797
Water25,3471407
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14870 Å2
ΔGint-144 kcal/mol
Surface area50810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.200, 167.000, 79.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PROTEIN (COPPER AMINE OXIDASE)


Mass: 80799.125 Da / Num. of mol.: 2 / Mutation: D383E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Description: ESCHERICHIA COLI PERIPLASM / Cellular location: PERIPLASM / Gene: maoA / Plasmid: PKK233-3 / Production host: Escherichia coli (E. coli) / References: UniProt: P46883, monoamine oxidase
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1407 / 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: 2.79 Å3/Da / Density % sol: 55.92 %
Crystal growTemperature: 315 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: VAPOR DIFFUSION, SITTING DROP PH 7.1, 315 K SODIUM CITRATE, HEPES
Crystal
*PLUS
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.3 Msodium citrate1reservoir
2100 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 21, 1997 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 92396 / Num. obs: 92396 / % possible obs: 91.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.9 % / Biso Wilson estimate: 30.2 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 8.3
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 1.03 % / Rmerge(I) obs: 0.204 / Mean I/σ(I) obs: 3.2 / % possible all: 73.3
Reflection
*PLUS
Num. obs: 84390

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4model building
REFMACrefinement
CCP4(SCALA)data scaling
CNSphasing
CCP4phasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: PDB ENTRY 1OAC

1oac


Resolution: 2.2→20 Å / SU B: 6.16638 / SU ML: 0.15259 / σ(F): 0 / σ(I): 0 / ESU R: 0.27486 / ESU R Free: 0.22699 / Stereochemistry target values: ENGH & HUBER / Details: USED SIGMA A WEIGHTED MAXIMUM LIKELIHOOD TARGETS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24429 2781 3.5 %RANDOM
Rwork0.1764 ---
all0.179 82076 --
obs0.179 92396 91.6 %-
Displacement parametersBiso mean: 32.227 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11356 0 12 1407 12775
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.01
X-RAY DIFFRACTIONp_angle_d0.0490.03
X-RAY DIFFRACTIONp_angle_deg3.6
X-RAY DIFFRACTIONp_planar_d0.0530.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it3.182
X-RAY DIFFRACTIONp_mcangle_it4.093
X-RAY DIFFRACTIONp_scbond_it4.0562
X-RAY DIFFRACTIONp_scangle_it5.5743
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.2130.15
X-RAY DIFFRACTIONp_singtor_nbd0.20.3
X-RAY DIFFRACTIONp_multtor_nbd0.2330.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1830.3
X-RAY DIFFRACTIONp_planar_tor1.37
X-RAY DIFFRACTIONp_staggered_tor1815
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor24.820
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 20 Å / Num. reflection all: 92396 / Num. reflection obs: 82076 / % reflection Rfree: 3.5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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