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- PDB-4e4z: Oxidized (Cu2+) peptidylglycine alpha-hydroxylating monooxygenase... -

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Basic information

Entry
Database: PDB / ID: 4e4z
TitleOxidized (Cu2+) peptidylglycine alpha-hydroxylating monooxygenase (PHM) in complex with hydrogen peroxide (1.98 A)
ComponentsPeptidyl-glycine alpha-amidating monooxygenase
KeywordsOXIDOREDUCTASE / Catalysis / Mixed Function Oxygenases / Multienzyme Complexes / Stereoisomerism
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
COPPER (II) ION / NICKEL (II) ION / HYDROGEN PEROXIDE / Peptidylglycine alpha-amidating monooxygenase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.98 Å
AuthorsRudzka, K. / Amzel, L.M.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2013
Title: Coordination of peroxide to the Cu(M) center of peptidylglycine alpha-hydroxylating monooxygenase (PHM): structural and computational study.
Authors: Rudzka, K. / Moreno, D.M. / Eipper, B. / Mains, R. / Estrin, D.A. / Amzel, L.M.
History
DepositionMar 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Peptidyl-glycine alpha-amidating monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3629
Polymers34,7741
Non-polymers5888
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.503, 68.513, 81.472
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Peptidyl-glycine alpha-amidating monooxygenase / PAM / Peptidylglycine alpha-hydroxylating monooxygenase / PHM / Peptidyl-alpha-hydroxyglycine alpha- ...PAM / Peptidylglycine alpha-hydroxylating monooxygenase / PHM / Peptidyl-alpha-hydroxyglycine alpha-amidating lyase / Peptidylamidoglycolate lyase / PAL


Mass: 34773.883 Da / Num. of mol.: 1 / Fragment: UNP residues 45-356
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Pam / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P14925, peptidylglycine monooxygenase

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Non-polymers , 5 types, 157 molecules

#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-PEO / HYDROGEN PEROXIDE / Hydrogen peroxide


Mass: 34.015 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O2
#5: 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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 55.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.97→25 Å / Num. obs: 26738 / % possible obs: 97.4 % / Redundancy: 11.8 % / Rmerge(I) obs: 0.063 / Χ2: 1.762 / Net I/σ(I): 14.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.97-29.40.69212911.453195.1
2-2.0410.30.62112761.451196.3
2.04-2.08110.60113131.515196.8
2.08-2.1211.70.5313201.482197.3
2.12-2.17120.44913091.515198.3
2.17-2.2212.20.38213221.592197.3
2.22-2.2712.30.32813361.617197.7
2.27-2.3412.40.29413241.634198.7
2.34-2.412.40.23213291.631198.7
2.4-2.4812.40.20113421.689198.1
2.48-2.5712.40.16113241.759198.3
2.57-2.6712.30.13613481.814198.6
2.67-2.7912.30.10113561.882198.8
2.79-2.9412.20.07713641.856198.8
2.94-3.1312.20.06313551.896198.4
3.13-3.3712.20.0513521.948199.3
3.37-3.712.10.0413821.848198.7
3.7-4.2411.80.03613711.905197.8
4.24-5.3311.50.03413552.008195.6
5.33-2510.70.0413692.633190.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.98→23.22 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 1 / SU B: 4.252 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2442 1351 5.1 %RANDOM
Rwork0.2043 ---
obs0.2063 26633 96.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 109.55 Å2 / Biso mean: 47.4079 Å2 / Biso min: 23.42 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å20 Å2-0 Å2
2---2.64 Å20 Å2
3---1.84 Å2
Refinement stepCycle: LAST / Resolution: 1.98→23.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2433 0 29 149 2611
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022537
X-RAY DIFFRACTIONr_angle_refined_deg1.2161.9583435
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6965311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.81923.148108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.81415392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3411515
X-RAY DIFFRACTIONr_chiral_restr0.0860.2374
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211932
LS refinement shellResolution: 1.976→2.027 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 75 -
Rwork0.277 1591 -
all-1666 -
obs--90.4 %

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