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

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Basic information

Entry
Database: PDB / ID: 6nck
TitleCrystal structure of H108A peptidylglycine alpha-hydroxylating monooxygenase (PHM)
ComponentsPeptidyl-glycine alpha-amidating monooxygenase
KeywordsHYDROLASE / PHM / peptidylglycine alpha-hydroxylating monooxygenase / PAL
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 / Peptidylglycine alpha-amidating monooxygenase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsMiller, M.S. / Maheshwari, S. / Gabelli, S.B.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA062924 United States
National Science Foundation (NSF, United States)MCB-1517522 United States
CitationJournal: Molecules / Year: 2019
Title: Getting the Most Out of Your Crystals: Data Collection at the New High-Flux, Microfocus MX Beamlines at NSLS-II.
Authors: Miller, M.S. / Maheshwari, S. / Shi, W. / Gao, Y. / Chu, N. / Soares, A.S. / Cole, P.A. / Amzel, L.M. / Fuchs, M.R. / Jakoncic, J. / Gabelli, S.B.
History
DepositionDec 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _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 11, 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_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.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_symmetry

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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)34,8293
Polymers34,7071
Non-polymers1222
Water36020
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)59.310, 65.880, 69.750
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 / Mutation: H108A
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, 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: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 1.96 Å3/Da / Density % sol: 37.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 19-24% PEG 4000, Tris HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.7→44.08 Å / Num. obs: 7872 / % possible obs: 99.6 % / Redundancy: 4.873 % / Biso Wilson estimate: 53.452 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.13 / Rrim(I) all: 0.145 / Χ2: 0.975 / Net I/σ(I): 8.19 / Num. measured all: 38364 / Scaling rejects: 36
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.7-2.774.0540.6062.685740.8150.69299.1
2.77-2.854.5910.4743.375310.9010.53499.4
2.85-2.934.9150.3664.195440.9350.408100
2.93-3.024.7390.3174.545320.9580.35699.4
3.02-3.125.3420.2675.925120.9580.296100
3.12-3.235.2390.2266.344930.9720.251100
3.23-3.355.3050.1857.674790.9760.204100
3.35-3.495.230.1618.434740.9820.178100
3.49-3.645.1550.1459.254390.9830.161100
3.64-3.825.1140.1349.884300.9860.149100
3.82-4.035.0320.12610.64090.9880.1499.5
4.03-4.275.0560.11511.783730.9870.12799.2
4.27-4.564.7930.10812.143720.9880.11999.7
4.56-4.934.6810.09912.213390.9910.11199.1
4.93-5.44.0940.09811.283200.9870.11299.4
5.4-6.044.4020.09811.552860.9880.11199.3
6.04-6.975.0240.09412.482550.9850.10599.2
6.97-8.545.0790.08813.482270.990.098100
8.54-12.084.7430.08213.551790.9950.09298.9
12.08-44.084.2120.08712.791040.990.09794.5
Serial crystallography sample deliveryMethod: fixed target

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.506
Highest resolutionLowest resolution
Rotation44.08 Å3.5 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6AO6

6ao6


Resolution: 2.7→44.08 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.871 / SU B: 18.766 / SU ML: 0.376 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.457
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2949 394 5 %RANDOM
Rwork0.2196 ---
obs0.2233 7477 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 134.89 Å2 / Biso mean: 54.282 Å2 / Biso min: 29.71 Å2
Baniso -1Baniso -2Baniso -3
1--2.87 Å20 Å20 Å2
2--7.85 Å20 Å2
3----4.98 Å2
Refinement stepCycle: final / Resolution: 2.7→44.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2350 0 2 20 2372
Biso mean--109.36 41.62 -
Num. residues----300
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132420
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172185
X-RAY DIFFRACTIONr_angle_refined_deg1.5411.6523291
X-RAY DIFFRACTIONr_angle_other_deg1.3461.5695071
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5135297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.07421.417120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.915381
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0211515
X-RAY DIFFRACTIONr_chiral_restr0.0680.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022693
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02524
LS refinement shellResolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 29 -
Rwork0.322 542 -
all-571 -
obs--99.13 %

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