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- PDB-6an3: Crystal structure of H172A-peptidylglycine alpha-hydroxylating mo... -

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Basic information

Entry
Database: PDB / ID: 6an3
TitleCrystal structure of H172A-peptidylglycine alpha-hydroxylating monooxygenase (PHM) mutant soaked with peptide (no CuH bound, no peptide bound)
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 / 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 copper ion / response to pH / L-ascorbic acid binding / limb development / response to zinc ion / transport vesicle membrane / 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 / copper ion binding / response to xenobiotic stimulus / 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
COPPER (II) ION / DI(HYDROXYETHYL)ETHER / Peptidylglycine alpha-amidating monooxygenase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
Model detailsCuM bound, no CuH, no peptide
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
DepositionAug 11, 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 6, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8763
Polymers34,7071
Non-polymers1702
Water3,171176
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)59.029, 66.847, 70.246
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 / Mutation: H172A
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


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.4 % / Mosaicity: 0.705 ° / Mosaicity esd: 0.007 °
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: Oct 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 17232 / % possible obs: 95.6 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.022 / Rrim(I) all: 0.055 / Χ2: 1.879 / Net I/σ(I): 20.8 / Num. measured all: 93871
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.05-2.0920.1456230.9550.1140.1861.01270.6
2.09-2.122.40.1387150.9720.0970.171.06180.4
2.12-2.162.80.1247380.9820.0810.1491.07685.8
2.16-2.213.30.148060.9790.0840.1641.01890.5
2.21-2.264.20.1098210.9810.0580.1241.3992.9
2.26-2.315.30.1188760.9920.0550.131.17197.7
2.31-2.375.90.1048500.9930.0470.1141.18996.3
2.37-2.435.90.0928850.9950.0410.1011.21399.6
2.43-2.560.0888700.9950.0390.0971.21298.5
2.5-2.586.10.0768870.9960.0330.0841.3899.8
2.58-2.686.20.0748910.9960.0320.0811.458100
2.68-2.786.30.0659040.9970.0280.0711.531100
2.78-2.916.50.0578890.9970.0240.0621.715100
2.91-3.066.60.0539010.9980.0220.0581.902100
3.06-3.256.60.058910.9980.0210.0552.109100
3.25-3.516.50.0489060.9980.020.0522.482100
3.51-3.866.40.0479150.9980.020.0522.786100
3.86-4.426.30.0439270.9980.0180.0472.767100
4.42-5.566.10.0439360.9980.0190.0472.947100
5.56-505.30.04310010.9980.020.0473.10399.3

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Processing

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

1phm


Resolution: 2.05→48.43 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.9 / WRfactor Rfree: 0.2783 / WRfactor Rwork: 0.1933 / FOM work R set: 0.7884 / SU B: 5.812 / SU ML: 0.16 / SU R Cruickshank DPI: 0.2732 / SU Rfree: 0.2373 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.273 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2817 858 5 %RANDOM
Rwork0.1969 ---
obs0.2011 16297 95.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 116.94 Å2 / Biso mean: 34.78 Å2 / Biso min: 14.77 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å20 Å2
2--1.38 Å20 Å2
3----0.88 Å2
Refinement stepCycle: final / Resolution: 2.05→48.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2375 0 8 176 2559
Biso mean--42.79 39.52 -
Num. residues----305
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192467
X-RAY DIFFRACTIONr_bond_other_d0.0020.022297
X-RAY DIFFRACTIONr_angle_refined_deg1.8741.9553355
X-RAY DIFFRACTIONr_angle_other_deg1.08435294
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0335305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.36922.925106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.1215386
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2171516
X-RAY DIFFRACTIONr_chiral_restr0.1210.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212761
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02571
LS refinement shellResolution: 2.052→2.105 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 39 -
Rwork0.205 909 -
all-948 -
obs--72.76 %

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