- PDB-3igh: Crystal structure of an uncharacterized metal-dependent hydrolase... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3igh
Title
Crystal structure of an uncharacterized metal-dependent hydrolase from pyrococcus horikoshii ot3
Components
UNCHARACTERIZED METAL-DEPENDENT HYDROLASE
Keywords
HYDROLASE / STRUCTURAL GENOMICS / AMIDOHYDROLASE / PSI-2 / PROTEIN STRUCTURE INITIATIVE / NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS / NYSGXRC
Function / homology
Function and homology information
endodeoxyribonuclease activity, producing 5'-phosphomonoesters / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds Similarity search - Function
Diaminopimelate Epimerase; Chain A, domain 1 - #70 / YtcJ like / TatD deoxyribonuclease family signature 1. / Deoxyribonuclease, TatD-related, conserved site / Amidohydrolase 3 / Amidohydrolase family / Diaminopimelate Epimerase; Chain A, domain 1 / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Metal-dependent hydrolase, composite domain superfamily ...Diaminopimelate Epimerase; Chain A, domain 1 - #70 / YtcJ like / TatD deoxyribonuclease family signature 1. / Deoxyribonuclease, TatD-related, conserved site / Amidohydrolase 3 / Amidohydrolase family / Diaminopimelate Epimerase; Chain A, domain 1 / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Metal-dependent hydrolase, composite domain superfamily / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel / Roll / Alpha-Beta Barrel / Mainly Beta / Alpha Beta Similarity search - Domain/homology
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9789 Å / Relative weight: 1
Reflection
Resolution: 1.95→50 Å / Num. obs: 56472 / % possible obs: 99.7 % / Observed criterion σ(I): -5 / Redundancy: 10.2 % / Biso Wilson estimate: 35.634 Å2 / Rsym value: 0.084 / Net I/σ(I): 6.5
Reflection shell
Resolution: 1.95→2.02 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 1 / % possible all: 99
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Processing
Software
Name
Version
Classification
SHELXD
phasing
REFMAC
5.3.0034
refinement
DENZO
datareduction
HKL-2000
datascaling
Refinement
Method to determine structure: SAD / Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.91 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.21234
1742
3.1 %
RANDOM
Rwork
0.17812
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-
-
obs
0.17915
54563
99.85 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 43.049 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.45 Å2
0 Å2
0 Å2
2-
-
-0.45 Å2
0 Å2
3-
-
-
0.89 Å2
Refinement step
Cycle: LAST / Resolution: 1.95→20 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3990
0
100
369
4459
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.008
0.022
4173
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.159
1.997
5682
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.212
5
533
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
33.29
23.743
187
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.389
15
784
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
15.021
15
31
X-RAY DIFFRACTION
r_chiral_restr
0.084
0.2
627
X-RAY DIFFRACTION
r_gen_planes_refined
0.004
0.02
3063
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
0.155
0.3
1922
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
0.299
0.5
2791
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.157
0.5
632
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.138
0.3
56
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.163
0.5
37
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
3.972
2
2554
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
5.008
3
4030
X-RAY DIFFRACTION
r_scbond_it
8.087
4
1806
X-RAY DIFFRACTION
r_scangle_it
11.259
6
1624
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 1.95→2 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.281
133
-
Rwork
0.249
3872
-
obs
-
-
98.84 %
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