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- PDB-1phm: PEPTIDYLGLYCINE ALPHA-HYDROXYLATING MONOOXYGENASE (PHM) FROM RAT -

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Basic information

Entry
Database: PDB / ID: 1phm
TitlePEPTIDYLGLYCINE ALPHA-HYDROXYLATING MONOOXYGENASE (PHM) FROM RAT
ComponentsPEPTIDYLGLYCINE ALPHA-HYDROXYLATING MONOOXYGENASE
KeywordsMONOOXYGENASE / BIOACTIVE PEPTIDE ACTIVATION / ASCORBATE / OXIDOREDUCTASE
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
AZIDE ION / COPPER (II) ION / Peptidylglycine alpha-amidating monooxygenase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsPrigge, S.T. / Amzel, L.M.
CitationJournal: Science / Year: 1997
Title: Amidation of bioactive peptides: the structure of peptidylglycine alpha-hydroxylating monooxygenase.
Authors: Prigge, S.T. / Kolhekar, A.S. / Eipper, B.A. / Mains, R.E. / Amzel, L.M.
History
DepositionOct 10, 1997Processing site: BNL
Revision 1.0Nov 11, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PEPTIDYLGLYCINE ALPHA-HYDROXYLATING MONOOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1799
Polymers34,5781
Non-polymers6018
Water4,071226
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.400, 68.660, 81.380
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 PEPTIDYLGLYCINE ALPHA-HYDROXYLATING MONOOXYGENASE / PEPTIDYLGLYCINE MONOOXYGENASE / PEPTIDYLGLYCINE 2-HYDROXYLASE / PHM


Mass: 34577.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: TWO BOUND COPPERS / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell line: DG44 / Organ: PITUITARY / Organelle: SECRETORY GRANULESecretion / Plasmid: PCIS / Cell line (production host): DG44 / Cellular location (production host): EXCRETED / Organ (production host): OVARY / Organelle (production host): SECRETORY VESICLES / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P14925, peptidylglycine monooxygenase
#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-AZI / AZIDE ION / Azide


Mass: 42.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: N3
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.75 Å3/Da / Density % sol: 50 % / Description: MAD AT CU K-EDGE
Crystal growpH: 5.5 / Details: pH 5.5
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 25 ℃ / Method: vapor diffusion, hanging drop / PH range low: 8 / PH range high: 5.25
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.525 mMcupric sulfate1reservoir
23.08 mM1reservoirNaN3
3100 mMdimethylarsinic acid1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9793
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Nov 1, 1997 / Details: SPHERICAL RH COATED MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 31034 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 33.1 Å2 / Rsym value: 0.045 / Net I/σ(I): 20.2
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 4.1 / Rsym value: 0.373 / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MADSYSphasing
X-PLOR3.8model building
X-PLOR3.8refinement
X-PLOR3.8phasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→6 Å / Rfactor Rfree error: 0.0071 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1369 5 %RANDOM
Rwork0.196 ---
obs0.196 27074 90.3 %-
Displacement parametersBiso mean: 41.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.2 Å
Luzzati d res low-6 Å
Refinement stepCycle: LAST / Resolution: 1.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2377 0 30 226 2633
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.079
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.548
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.21.5
X-RAY DIFFRACTIONx_mcangle_it3.62
X-RAY DIFFRACTIONx_scbond_it3.82
X-RAY DIFFRACTIONx_scangle_it5.52.5
LS refinement shellResolution: 1.9→1.95 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.291 94 3.8 %
Rwork0.286 1621 -
obs--70 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.548

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