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 / mitotic chromosome condensation / L-ascorbic acid binding / response to pH / response to copper ion / limb development / transport vesicle membrane / response to zinc ion / 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 / response to xenobiotic stimulus / copper ion binding / neuronal cell body / calcium ion binding / chromatin 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
Peptidylglycine alpha-hydroxylating monooxygenase/peptidyl-hydroxyglycine alpha-amidating lyase / 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. ...Peptidylglycine alpha-hydroxylating monooxygenase/peptidyl-hydroxyglycine alpha-amidating lyase / 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 / TolB, C-terminal domain / Six-bladed beta-propeller, TolB-like / 6 Propeller / Neuraminidase / Mainly Beta Similarity search - Domain/homology
Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 9, 2008 / Details: Monochromator Kohzu HLD-4 Double Crystal
Radiation
Monochromator: Kohzu HLD-4 Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.00724 Å / Relative weight: 1
Reflection
Resolution: 2.5→59.34 Å / Num. all: 13347 / Num. obs: 13347 / % possible obs: 99.6 % / Redundancy: 6.8 % / Rsym value: 0.075 / Net I/σ(I): 23.5
Reflection shell
Resolution: 2.5→2.59 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 1306 / Rsym value: 0.48 / % possible all: 98.9
-
Processing
Software
Name
Version
Classification
AMoRE
phasing
REFMAC
5.2.0019
refinement
HKL-2000
datareduction
HKL-2000
datascaling
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: PALcc native, being deposited at the same time as this structure Resolution: 2.52→59.34 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.899 / SU B: 18.474 / SU ML: 0.216 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.689 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.26019
655
4.9 %
RANDOM
Rwork
0.20672
-
-
-
obs
0.20939
12648
99.09 %
-
all
-
13347
-
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 44.912 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.12 Å2
0 Å2
0 Å2
2-
-
0.24 Å2
0 Å2
3-
-
-
-1.36 Å2
Refinement step
Cycle: LAST / Resolution: 2.52→59.34 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2619
0
17
118
2754
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.008
0.021
2721
X-RAY DIFFRACTION
r_angle_refined_deg
1.246
1.926
3694
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.552
5
330
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
37.247
24.317
139
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
17.925
15
413
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
19.785
15
11
X-RAY DIFFRACTION
r_chiral_restr
0.115
0.2
385
X-RAY DIFFRACTION
r_gen_planes_refined
0.003
0.02
2155
X-RAY DIFFRACTION
r_nbd_refined
0.195
0.2
1170
X-RAY DIFFRACTION
r_nbtor_refined
0.31
0.2
1762
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.126
0.2
136
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.167
0.2
51
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.224
0.2
8
X-RAY DIFFRACTION
r_mcbond_it
0.31
1.5
1676
X-RAY DIFFRACTION
r_mcangle_it
0.541
2
2664
X-RAY DIFFRACTION
r_scbond_it
1.213
3
1163
X-RAY DIFFRACTION
r_scangle_it
1.237
4.5
1030
LS refinement shell
Resolution: 2.515→2.58 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.404
48
-
Rwork
0.274
846
-
obs
-
1306
92.64 %
+
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