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- PDB-5wja: Crystal structure of H107A peptidylglycine alpha-hydroxylating mo... -

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Basic information

Entry
Database: PDB / ID: 5wja
TitleCrystal structure of H107A peptidylglycine alpha-hydroxylating monooxygenase (PHM) in complex with citrate
ComponentsPeptidyl-glycine alpha-amidating monooxygenase
KeywordsOXIDOREDUCTASE / PEPTIDYLGLYCINE MONOOXYGENASE / PEPTIDYLGLYCINE 2-HYDROXYLASE / PHM / METAL BINDING PROTEIN / LYASE
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
COPPER (II) ION / CITRATE ANION / NICKEL (II) ION / Peptidylglycine alpha-amidating monooxygenase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
Model detailscopper M is present in both molecules: copper H is present in only one molecule
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
DepositionJul 21, 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.4Oct 30, 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
D: Peptidyl-glycine alpha-amidating monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,40513
Polymers69,4142
Non-polymers99111
Water2,558142
1
A: Peptidyl-glycine alpha-amidating monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,44510
Polymers34,7071
Non-polymers7389
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Peptidyl-glycine alpha-amidating monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9593
Polymers34,7071
Non-polymers2532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.544, 100.613, 101.582
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, 2 molecules AD

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


Mass: 34706.812 Da / Num. of mol.: 2 / Fragment: PHM / Mutation: H107A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Pam / Plasmid: PCIS / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHO
References: UniProt: P14925, peptidylglycine monooxygenase, peptidylamidoglycolate lyase

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Non-polymers , 5 types, 153 molecules

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


Mass: 63.546 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#5: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.19 Å3/Da / Density % sol: 43.88 % / Mosaicity: 0.72 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5 / Details: 19-24% PEG 4000, Tris HCL, citrate

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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: Jul 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→29.77 Å / Num. obs: 27694 / % possible obs: 99.6 % / Redundancy: 1.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.048 / Rrim(I) all: 0.069 / Net I/σ(I): 9.6 / Num. measured all: 52974 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.3-2.381.90.339501625910.8280.3390.4792.396.3
8.91-29.771.70.0289255380.9960.0280.0419.497.1

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Processing

Software
NameVersionClassification
REFMACrefinement
DENZOdata collection
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PHM

1phm


Resolution: 2.3→29.77 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.922 / WRfactor Rfree: 0.2799 / WRfactor Rwork: 0.201 / FOM work R set: 0.7566 / SU B: 10.497 / SU ML: 0.244 / SU R Cruickshank DPI: 0.4148 / SU Rfree: 0.2795 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.415 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2732 1390 5 %RANDOM
Rwork0.1979 ---
obs0.2017 26271 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 148.68 Å2 / Biso mean: 51.392 Å2 / Biso min: 17.72 Å2
Baniso -1Baniso -2Baniso -3
1-4.6 Å2-0 Å20 Å2
2---3.16 Å2-0 Å2
3----1.45 Å2
Refinement stepCycle: final / Resolution: 2.3→29.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4798 0 53 142 4993
Biso mean--60.91 46.18 -
Num. residues----616
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194997
X-RAY DIFFRACTIONr_bond_other_d0.0020.024508
X-RAY DIFFRACTIONr_angle_refined_deg1.781.966796
X-RAY DIFFRACTIONr_angle_other_deg1.053310471
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8835618
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.07123.146213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.59315779
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9791530
X-RAY DIFFRACTIONr_chiral_restr0.1360.2739
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215537
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021037
LS refinement shellResolution: 2.301→2.361 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 98 -
Rwork0.293 1815 -
all-1913 -
obs--95.17 %

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