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- PDB-1yjl: Reduced Peptidylglycine alpha-Hydroxylating Monooxygenase in a ne... -

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Basic information

Entry
Database: PDB / ID: 1yjl
TitleReduced Peptidylglycine alpha-Hydroxylating Monooxygenase in a new crystal form
ComponentsPeptidyl-glycine alpha-amidating monooxygenase
KeywordsOXIDOREDUCTASE / MONOOXYGENASE / BIOACTIVE PEPTIDE ACTIVATION / COPPER / 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 / response to pH / mitotic chromosome condensation / 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
Peptidylglycine alpha-amidating monooxygenase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 14, 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: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
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

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Assembly

Deposited unit
A: Peptidyl-glycine alpha-amidating monooxygenase


Theoretical massNumber of molelcules
Total (without water)34,1401
Polymers34,1401
Non-polymers00
Water82946
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.764, 66.019, 69.526
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: 34140.145 Da / Num. of mol.: 1
Fragment: Peptidylglycine alpha-Hydroxylating Monooxygenase (Residues 50-355)
Mutation: y
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.5 Å3/Da / Density % sol: 50 %
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: Mar 7, 2004 / Details: MIRRORS
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionRedundancy: 4.46 % / Number: 49868 / Rmerge(I) obs: 0.065 / D res high: 2.4 Å / D res low: 65.94 Å
Refln sys abs
Index hIndex kIndex lI I/σ(I)σ(I)
0038.913.12.92
0058.212.33.58
0079.72.34.25
00911.072.34.71
00118.0924.11
001321.073.16.7
001513.752.26.22
001718.322.37.92
001936.065.96.09
002131.083.29.86
002323.6638.02
002524.452.88.77
002717.952.18.41
0305.982.12.87
0509.252.24.28
07013.262.65.12
09024.133.56.95
011016.351.610.06
013020.251.513.45
015012.521.48.89
017043.552.220.16
019016.231.411.92
021033.072.215.11
023036.23218.54
027023.51.515.37
3009.213.62.54
5008.112.13.84
70012.832.94.38
110019.362.86.83
130011.931.77.05
150023.953.27.46
190011.061.67
ReflectionResolution: 2.4→65.94 Å / Num. all: 11174 / Num. obs: 11174 / % possible obs: 99.5 % / Observed criterion σ(F): -3.7 / Redundancy: 4.5 % / Biso Wilson estimate: 51.3 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 4.3
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 1.7 / Num. measured all: 7310 / Num. unique all: 1577 / Rsym value: 0.445 / % possible all: 99.68

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Processing

Software
NameVersionClassificationNB
SCALACCP4_3.2.5data scaling
REFMACrefinement
PDB_EXTRACT1.501data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OPM

1opm


Resolution: 2.4→47.67 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.905 / SU B: 20.045 / SU ML: 0.228 / SU R Cruickshank DPI: 0.635 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.274 535 4.8 %RANDOM
Rwork0.206 ---
all0.209 11141 --
obs0.209 11141 99.28 %-
Solvent computationSolvent model: MASK
Displacement parametersBiso mean: 50.951 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20 Å20 Å2
2--1.68 Å20 Å2
3----2.32 Å2
Refinement stepCycle: LAST / Resolution: 2.4→47.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2245 0 0 46 2291
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONr_bond_refined_d0.02123150.022
X-RAY DIFFRACTIONr_angle_refined_deg1.92731531.934
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8242825
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.9429922.828
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.17936115
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3141415
X-RAY DIFFRACTIONr_chiral_restr0.1343430.2
X-RAY DIFFRACTIONr_gen_planes_refined0.00817730.02
X-RAY DIFFRACTIONr_nbd_refined0.2358830.2
X-RAY DIFFRACTIONr_nbtor_refined0.31815200.2
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1871030.2
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.27510.2
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.24960.2
X-RAY DIFFRACTIONr_mcbond_it1.05314631.5
X-RAY DIFFRACTIONr_mcangle_it1.76523242
X-RAY DIFFRACTIONr_scbond_it2.3449853
X-RAY DIFFRACTIONr_scangle_it3.4968294.5
LS refinement shellResolution: 2.4→2.462 Å
RfactorNum. reflection% reflection
Rfree0.406 33 -
Rwork0.244 760 -
obs--99.5 %
Refinement TLS params.Method: refined / Origin x: 30.312 Å / Origin y: 7.217 Å / Origin z: 19.914 Å
111213212223313233
T-0.1406 Å2-0.0015 Å2-0.0433 Å2--0.1084 Å20.0209 Å2---0.1147 Å2
L1.9339 °2-0.5358 °2-1.6069 °2-1.2777 °20.5027 °2--5.7716 °2
S0.0311 Å °0.1981 Å °-0.0723 Å °-0.2431 Å °-0.0292 Å °0.3358 Å °-0.0564 Å °-0.6073 Å °-0.0019 Å °
Refinement TLS groupSelection: ALL

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