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- PDB-1yip: Oxidized Peptidylglycine Alpha-Hydroxylating Monooxygenase (PHM) ... -

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Basic information

Entry
Database: PDB / ID: 1yip
TitleOxidized Peptidylglycine Alpha-Hydroxylating Monooxygenase (PHM) 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 / mitotic chromosome condensation / L-ascorbic acid binding / response to pH / response to copper ion / limb development / transport vesicle membrane / response to zinc ion / maternal process involved in female pregnancy / response to glucocorticoid / condensed chromosome / 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 / calcium ion binding / chromatin 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 / MOLECULAR REPLACEMENT / Resolution: 2.2 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 12, 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 1.3Aug 23, 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 / pdbx_struct_conn_angle / struct_conn / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)34,8023
Polymers34,6751
Non-polymers1272
Water2,846158
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.523, 65.683, 69.871
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: 34674.754 Da / Num. of mol.: 1
Fragment: Peptidylglycine alpha-Hydroxylating Monooxygenase (Residues 45-355)
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


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 2, 2004 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionRedundancy: 4.69 % / Number: 65926 / Rmerge(I) obs: 0.101 / D res high: 2.2 Å / D res low: 30.01 Å
Refln sys abs
Index hIndex kIndex lI I/σ(I)σ(I)
002553.18226.17
002727.411.518.73
002927.661.518.65
003152.831.633.02
03018.52.67.03
05024.882.69.48
07022.772.210.37
09021.192.110.31
011035.642.414.77
013026.751.616.77
015036.91.623.2
017046.471.629.62
019020.391.414.22
021064.442.130.98
023048.241.728.05
025054.53.117.5
027043.811.726.01
029030.551.421.13
30016.92.56.67
50026.833.38.09
70017.982.18.54
90020.372.19.73
110041.162.814.53
130055.215.110.88
150048.372.221.55
170046.32.121.71
190034.15217.32
210053.542.323.29
230045.812.221.08
250036.512.315.87
ReflectionResolution: 2.2→30.01 Å / Num. all: 14064 / Num. obs: 14064 / % possible obs: 92.9 % / Observed criterion σ(I): -3.7 / Redundancy: 4.7 % / Biso Wilson estimate: 38.84 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 12.04
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 2.18 / Num. measured all: 9440 / Num. unique all: 2026 / Rsym value: 0.444 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SCALACCP4_5.0data scaling
REFMACrefmac_5.2.0003refinement
PDB_EXTRACT1.501data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OPM

1opm


Resolution: 2.2→30.01 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.239 / WRfactor Rwork: 0.189 / SU B: 13.954 / SU ML: 0.187 / SU R Cruickshank DPI: 0.394 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(I): 2 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2389 687 4.895 %RANDOM
Rwork0.1895 ---
all0.192 14034 --
obs0.192 14034 98.908 %-
Solvent computationSolvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 38.582 Å2
Baniso -1Baniso -2Baniso -3
1--2.59 Å20 Å20 Å2
2--2.739 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2425 0 2 158 2585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222499
X-RAY DIFFRACTIONr_bond_other_d0.0010.022213
X-RAY DIFFRACTIONr_angle_refined_deg1.8221.9343403
X-RAY DIFFRACTIONr_angle_other_deg0.91335151
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5425310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.56323.148108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.26615391
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9491515
X-RAY DIFFRACTIONr_chiral_restr0.1130.2368
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022785
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02519
X-RAY DIFFRACTIONr_nbd_refined0.2350.2487
X-RAY DIFFRACTIONr_nbd_other0.1950.22328
X-RAY DIFFRACTIONr_nbtor_refined0.1880.21142
X-RAY DIFFRACTIONr_nbtor_other0.0920.21540
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2130.2150
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1360.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1890.287
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2080.217
X-RAY DIFFRACTIONr_mcbond_it1.1211.51953
X-RAY DIFFRACTIONr_mcbond_other0.211.5625
X-RAY DIFFRACTIONr_mcangle_it1.38322524
X-RAY DIFFRACTIONr_mcangle_other0.63222112
X-RAY DIFFRACTIONr_scbond_it2.20531110
X-RAY DIFFRACTIONr_scbond_other0.87631991
X-RAY DIFFRACTIONr_scangle_it3.1734.5879
X-RAY DIFFRACTIONr_scangle_other1.3094.53039
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.2570.284400.2259841024100
2.257-2.3190.292460.231951997100
2.319-2.3860.283550.207920975100
2.386-2.4590.318400.228904944100
2.459-2.5390.262410.232878919100
2.539-2.6280.286380.215852890100
2.628-2.7270.306390.211812851100
2.727-2.8380.29460.217793839100
2.838-2.9640.299460.20476381099.877
2.964-3.1080.25430.18471676199.737
3.108-3.2750.29340.19369573599.184
3.275-3.4730.173300.17465669199.276
3.473-3.7110.221280.16762566198.79
3.711-4.0070.208300.16958062098.387
4.007-4.3860.144310.14851856497.34
4.386-4.8990.268340.15647252097.308
4.899-5.6460.179260.18741345995.643
5.646-6.8910.233200.20636140394.541
6.891-9.6460.201100.19728832392.26
9.646-47.6730.256100.20616620386.7
Refinement TLS params.Method: refined / Origin x: 57.8041 Å / Origin y: 7.0705 Å / Origin z: 19.9527 Å
111213212223313233
T-0.089 Å20.0131 Å2-0.0244 Å2--0.1678 Å2-0.0095 Å2---0.0646 Å2
L0.9038 °2-0.0958 °2-0.3645 °2-0.4888 °20.1885 °2--1.9576 °2
S-0.0144 Å °0.1072 Å °-0.0404 Å °-0.0722 Å °-0.018 Å °0.078 Å °-0.0707 Å °-0.1908 Å °0.0324 Å °
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Refine TLS-ID: 1 / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDAuth seq-IDLabel seq-ID
147 - 2003 - 156
2201 - 354157 - 310

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