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- PDB-1yi9: Crystal Structure Analysis of the oxidized form of the M314I muta... -

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Basic information

Entry
Database: PDB / ID: 1yi9
TitleCrystal Structure Analysis of the oxidized form of the M314I mutant of Peptidylglycine alpha-Hydroxylating Monooxygenase
ComponentsPeptidyl-glycine alpha-amidating monooxygenase
KeywordsOXIDOREDUCTASE / MONOOXYGENASE / BIOACTIVE PEPTIDE ACTIVATION / ASCORBATE
Function / homology
Function and homology information


peptidylglycine monooxygenase / peptidylamidoglycolate lyase / peptide amidation / peptidylglycine monooxygenase activity / peptidylamidoglycolate lyase activity / fatty acid primary amide biosynthetic process / toxin metabolic process / ovulation cycle process / long-chain fatty acid metabolic process / peptide metabolic process ...peptidylglycine monooxygenase / peptidylamidoglycolate lyase / peptide amidation / peptidylglycine monooxygenase activity / peptidylamidoglycolate lyase activity / fatty acid primary amide biosynthetic process / toxin metabolic process / ovulation cycle process / long-chain fatty acid metabolic process / peptide metabolic process / mitotic chromosome condensation / response to pH / L-ascorbic acid binding / response to copper ion / limb development / transport vesicle membrane / response to zinc ion / maternal process involved in female pregnancy / condensed chromosome / response to glucocorticoid / lactation / secretory granule / regulation of actin cytoskeleton organization / trans-Golgi network / response to estradiol / heart development / perikaryon / response to hypoxia / response to xenobiotic stimulus / copper ion binding / neuronal cell body / chromatin binding / calcium ion binding / chromatin / regulation of transcription by RNA polymerase II / protein kinase binding / perinuclear region of cytoplasm / cell surface / extracellular space / zinc ion binding / extracellular region / identical protein binding
Similarity search - Function
Copper type II, ascorbate-dependent monooxygenase, N-terminal domain / Peptidylglycine alpha-hydroxylating monooxygenase/peptidyl-hydroxyglycine alpha-amidating lyase / Jelly Rolls - #230 / Copper type II, ascorbate-dependent monooxygenase, histidine-cluster-2 conserved site / Copper type II, ascorbate-dependent monooxygenases signature 2. / Copper type II, ascorbate-dependent monooxygenase, N-terminal / Copper type II, ascorbate-dependent monooxygenase, histidine-cluster-1 conserved site / Copper type II ascorbate-dependent monooxygenase, C-terminal / Copper type II, ascorbate-dependent monooxygenase, N-terminal domain superfamily / Copper type II ascorbate-dependent monooxygenase, N-terminal domain ...Copper type II, ascorbate-dependent monooxygenase, N-terminal domain / Peptidylglycine alpha-hydroxylating monooxygenase/peptidyl-hydroxyglycine alpha-amidating lyase / Jelly Rolls - #230 / Copper type II, ascorbate-dependent monooxygenase, histidine-cluster-2 conserved site / Copper type II, ascorbate-dependent monooxygenases signature 2. / Copper type II, ascorbate-dependent monooxygenase, N-terminal / Copper type II, ascorbate-dependent monooxygenase, histidine-cluster-1 conserved site / Copper type II ascorbate-dependent monooxygenase, C-terminal / Copper type II, ascorbate-dependent monooxygenase, N-terminal domain superfamily / Copper type II ascorbate-dependent monooxygenase, N-terminal domain / Copper type II ascorbate-dependent monooxygenase, C-terminal domain / Copper type II, ascorbate-dependent monooxygenases signature 1. / PHM/PNGase F domain superfamily / Copper type II, ascorbate-dependent monooxygenase-like, C-terminal / NHL repeat profile. / NHL repeat / NHL repeat / Six-bladed beta-propeller, TolB-like / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Peptidylglycine alpha-amidating monooxygenase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSiebert, X. / Eipper, B.A. / Mains, R.E. / Prigge, S.T. / Blackburn, N.J. / Amzel, L.M.
CitationJournal: Biophys.J. / Year: 2005
Title: The catalytic copper of Peptidylglycine alpha-Hydroxylating Monooxygenase also plays a critical structural role.
Authors: Siebert, X. / Eipper, B.A. / Mains, R.E. / Prigge, S.T. / Blackburn, N.J. / Amzel, L.M.
History
DepositionJan 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 20, 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.pdbx_dist_value / _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_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 23, 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: Peptidyl-glycine alpha-amidating monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8527
Polymers34,4141
Non-polymers4386
Water2,378132
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.479, 66.458, 70.049
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 Peptidyl-glycine alpha-amidating monooxygenase / PAM


Mass: 34413.500 Da / Num. of mol.: 1
Fragment: Peptidylglycine alpha-Hydroxylating Monooxygenase (Residues 47-355)
Mutation: M314I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Pam / Plasmid: PCIS / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): DG44 / References: UniProt: P14925, peptidylglycine monooxygenase
#2: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / 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 Å3/Da / Density % sol: 37.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, magnesium chloride, Tris , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 21, 2003 / Details: mirrors
RadiationMonochromator: DOUBLE SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.7→48.2 Å / Num. all: 61959 / Num. obs: 28704 / % possible obs: 87.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Biso Wilson estimate: 41.7 Å2 / Rmerge(I) obs: 0.041 / Rsym value: 0.041 / Net I/σ(I): 8.8
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 1.8 / Num. unique all: 3006 / Rsym value: 0.375 / % possible all: 48.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OPM

1opm


Resolution: 1.7→48.2 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 6.359 / SU ML: 0.101 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23261 1377 5.1 %RANDOM
Rwork0.2007 ---
all0.20239 61959 --
obs0.20239 25769 86.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 41.687 Å2
Baniso -1Baniso -2Baniso -3
1-0.76 Å20 Å20 Å2
2--0.21 Å20 Å2
3----0.96 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.13 Å0.143 Å
Refinement stepCycle: LAST / Resolution: 1.7→48.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2313 0 16 132 2461
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0222402
X-RAY DIFFRACTIONr_bond_other_d0.0050.022137
X-RAY DIFFRACTIONr_angle_refined_deg2.1821.9413259
X-RAY DIFFRACTIONr_angle_other_deg1.05834971
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5395293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.82123.039102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.30215373
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6991514
X-RAY DIFFRACTIONr_chiral_restr0.1480.2352
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022643
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02496
X-RAY DIFFRACTIONr_nbd_refined0.2350.2482
X-RAY DIFFRACTIONr_nbd_other0.2140.22165
X-RAY DIFFRACTIONr_nbtor_refined0.1950.21144
X-RAY DIFFRACTIONr_nbtor_other0.0990.21521
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.2141
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1490.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3830.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2650.270
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.213
X-RAY DIFFRACTIONr_mcbond_it2.0231.51833
X-RAY DIFFRACTIONr_mcbond_other0.4321.5590
X-RAY DIFFRACTIONr_mcangle_it2.35222402
X-RAY DIFFRACTIONr_scbond_it3.5431086
X-RAY DIFFRACTIONr_scangle_it4.644.5857
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 50 -
Rwork0.278 890 -
obs--41.5 %
Refinement TLS params.Method: refined / Origin x: 29.9607 Å / Origin y: 25.8268 Å / Origin z: 49.9494 Å
111213212223313233
T-0.1511 Å2-0.0085 Å20.0368 Å2--0.169 Å20.0122 Å2---0.1106 Å2
L1.4408 °20.5043 °20.7632 °2-1.2311 °21.023 °2--3.4478 °2
S0.0477 Å °-0.1796 Å °0.0761 Å °0.2003 Å °-0.1092 Å °0.1871 Å °0.1039 Å °-0.3446 Å °0.0615 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA47 - 2001 - 154
2X-RAY DIFFRACTION1AA201 - 355155 - 309

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