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- PDB-6ay0: Crystal structure of H108A peptidylglycine alpha-hydroxylating mo... -

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Basic information

Entry
Database: PDB / ID: 6ay0
TitleCrystal structure of H108A peptidylglycine alpha-hydroxylating monooxygenase (PHM) soaked with peptide
ComponentsPeptidyl-glycine alpha-amidating monooxygenase
KeywordsOXIDOREDUCTASE / PEPTIDYLGLYCINE MONOOXYGENASE / PEPTIDYLGLYCINE 2-HYDROXYLASE / PHM
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 / Peptidylglycine alpha-amidating monooxygenase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
Model detailsCuH absent, CuM present, No peptide density
AuthorsMaheshwari, S. / Rudzka, K. / Gabelli, S.B. / Amzel, L.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1517522 United States
CitationJournal: Commun Biol / Year: 2018
Title: Effects of copper occupancy on the conformational landscape of peptidylglycine alpha-hydroxylating monooxygenase.
Authors: Maheshwari, S. / Shimokawa, C. / Rudzka, K. / Kline, C.D. / Eipper, B.A. / Mains, R.E. / Gabelli, S.B. / Blackburn, N. / Amzel, L.M.
History
DepositionSep 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)34,7702
Polymers34,7071
Non-polymers641
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.808, 66.532, 70.217
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Peptidyl-glycine alpha-amidating monooxygenase / PAM


Mass: 34706.812 Da / Num. of mol.: 1 / Fragment: PHM
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Pam / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHO
References: UniProt: P14925, peptidylglycine monooxygenase, peptidylamidoglycolate lyase
#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 1.98 Å3/Da / Density % sol: 37.85 % / Mosaicity: 0.736 ° / Mosaicity esd: 0.008 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5 / Details: 19-24% PEG 4000, Tris HCL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Dec 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 9437 / % possible obs: 94.5 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.028 / Rrim(I) all: 0.069 / Χ2: 2.583 / Net I/σ(I): 19.9 / Num. measured all: 58408
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.545.50.1293490.9880.0570.1421.19669
2.54-2.595.60.1154120.9910.050.1261.23586.9
2.59-2.646.10.1234470.9890.0530.1351.22391.6
2.64-2.696.20.1114590.9930.0480.1211.3392.9
2.69-2.756.30.1084530.9930.0470.1181.48594.8
2.75-2.826.30.0954580.9950.0410.1041.55193.9
2.82-2.896.50.0854580.9950.0360.0921.57394.8
2.89-2.966.40.0834700.9960.0350.091.73994.6
2.96-3.056.60.0784780.9950.0330.0851.9995
3.05-3.156.60.0714530.9970.030.0772.02695.6
3.15-3.266.70.0714690.9960.0290.0772.21694.4
3.26-3.396.60.0644930.9960.0270.072.4499.4
3.39-3.556.50.0634890.9980.0270.0692.9897.4
3.55-3.736.20.074730.9940.030.0764.42997.3
3.73-3.976.30.0614930.9970.0260.0663.50198.6
3.97-4.276.40.0594920.9970.0250.0643.76298.8
4.27-4.76.10.0585100.9960.0250.0644.36998.5
4.7-5.386.10.0545110.9970.0240.063.77398.6
5.38-6.785.90.0575110.9950.0260.0633.65199.4
6.78-5050.0515590.9960.0250.0574.06797.6

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Processing

Software
NameVersionClassification
REFMACrefinement
DENZOdata collection
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
Cootmodel building
REFMACmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PHM

1phm


Resolution: 2.6→48.3 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.881 / WRfactor Rfree: 0.2658 / WRfactor Rwork: 0.1917 / FOM work R set: 0.8103 / SU B: 12.272 / SU ML: 0.266 / SU Rfree: 0.3912 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.391 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2658 407 4.8 %RANDOM
Rwork0.1917 ---
obs0.1953 8153 96.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 119.3 Å2 / Biso mean: 37.254 Å2 / Biso min: 11.95 Å2
Baniso -1Baniso -2Baniso -3
1--1.05 Å20 Å20 Å2
2--2.92 Å2-0 Å2
3----1.87 Å2
Refinement stepCycle: final / Resolution: 2.6→48.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2403 0 1 41 2445
Biso mean--67.47 28.81 -
Num. residues----309
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192498
X-RAY DIFFRACTIONr_bond_other_d0.0020.022255
X-RAY DIFFRACTIONr_angle_refined_deg1.8121.9543406
X-RAY DIFFRACTIONr_angle_other_deg1.05535239
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4875314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.89223.056108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.81215393
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.9331516
X-RAY DIFFRACTIONr_chiral_restr0.1020.2369
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212791
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02525
LS refinement shellResolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 29 -
Rwork0.206 554 -
all-583 -
obs--91.96 %

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