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- PDB-5wm0: Crystal structure of apo wild type peptidylglycine alpha-hydroxyl... -

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Basic information

Entry
Database: PDB / ID: 5wm0
TitleCrystal structure of apo wild type peptidylglycine alpha-hydroxylating monooxygenase (PHM) soaked with peptide (peptide not observed)
ComponentsPeptidyl-glycine alpha-amidating monooxygenase
KeywordsOXIDOREDUCTASE / PEPTIDYLGLYCINE MONOOXYGENASE / PEPTIDYLGLYCINE 2-HYDROXYLASE / PHM / METAL BINDING PROTEIN
Function / homology
Function and homology information


peptidylglycine monooxygenase / peptidylamidoglycolate lyase / peptide amidation / peptidylglycine monooxygenase activity / peptidylamidoglycolate lyase activity / fatty acid primary amide biosynthetic process / ovulation cycle process / toxin metabolic 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 / ovulation cycle process / toxin metabolic process / long-chain fatty acid metabolic process / peptide metabolic process / mitotic chromosome condensation / response to pH / L-ascorbic acid binding / limb development / response to zinc ion / response to copper ion / transport vesicle membrane / maternal process involved in female pregnancy / condensed chromosome / lactation / response to glucocorticoid / 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 / regulation of transcription by RNA polymerase II / protein kinase binding / chromatin / perinuclear region of cytoplasm / cell surface / extracellular space / extracellular region / zinc ion binding / 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 / FOURIER SYNTHESIS / Resolution: 2.4 Å
Model detailsno copper bound
AuthorsMaheshwari, S. / Rudzka, K. / Gabelli, S.B. / Amzel, L.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)0920288 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
DepositionJul 28, 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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)108,8101
Polymers108,8101
Non-polymers00
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.099, 65.930, 69.809
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: 108810.148 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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

CrystalMosaicity: 1.141 ° / Mosaicity esd: 0.02 °
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: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 11068 / % possible obs: 99.2 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.034 / Rrim(I) all: 0.082 / Χ2: 2.251 / Net I/σ(I): 15.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.442.60.3294610.8430.2320.4050.92988.1
2.44-2.4930.3545230.8680.2340.4280.93796.1
2.49-2.533.50.3085610.9090.1840.3611.00399.1
2.53-2.594.40.2675460.9550.1390.3031.08599.8
2.59-2.645.40.285280.9570.130.311.095100
2.64-2.75.70.2355430.9730.1060.2581.114100
2.7-2.775.80.2165670.9740.0970.2371.26100
2.77-2.855.90.1765350.980.0790.1931.364100
2.85-2.935.90.1435570.9880.0630.1571.5100
2.93-3.026.10.1325470.9910.0580.1451.443100
3.02-3.136.20.1165610.9910.050.1261.826100
3.13-3.266.30.15380.9920.0430.1091.965100
3.26-3.416.40.0885680.9950.0370.0952.347100
3.41-3.586.40.0795430.9950.0340.0872.542100
3.58-3.816.40.0725710.9960.030.0782.818100
3.81-4.16.30.0685600.9970.0290.0743.187100
4.1-4.526.20.0615640.9960.0260.0673.696100
4.52-5.1760.0575770.9970.0250.0623.69999.8
5.17-6.515.80.0575840.9960.0260.0633.35100
2.4-2.4624.90.0566340.9960.0290.0634.69599.7

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Processing

Software
NameVersionClassification
DENZOdata collection
SCALEPACKdata scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1PHM

1phm


Resolution: 2.4→47.93 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.898 / SU B: 11.01 / SU ML: 0.258 / SU R Cruickshank DPI: 0.934 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.934 / ESU R Free: 0.333
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2811 562 5.1 %RANDOM
Rwork0.1997 ---
obs0.2039 10468 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 164.8 Å2 / Biso mean: 51.291 Å2 / Biso min: 23.93 Å2
Baniso -1Baniso -2Baniso -3
1--1.15 Å20 Å20 Å2
2--2.73 Å2-0 Å2
3----1.58 Å2
Refinement stepCycle: final / Resolution: 2.4→47.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2413 0 0 27 2440
Biso mean---41.22 -
Num. residues----309
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192496
X-RAY DIFFRACTIONr_bond_other_d0.0020.022246
X-RAY DIFFRACTIONr_angle_refined_deg1.9331.9533397
X-RAY DIFFRACTIONr_angle_other_deg1.12935218
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6585309
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.87523.148108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.31115389
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5561515
X-RAY DIFFRACTIONr_chiral_restr0.1160.2368
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212771
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02520
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 37 -
Rwork0.258 682 -
all-719 -
obs--89.54 %

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