Biological unit contains protein chains A and B, DNA strands C and D. THE TETRAMER (ACCORDING TO PDB CONVENTIONS) IS A COMPLEX OF THE DIMERIC RESTRICTION ENZYME WITH ITS SUBSTRATE, DOUBLE STRANDED DNA.
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Components
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Protein , 1 types, 2 molecules AB
#1: Protein
RestrictionendonucleaseHpy99I
Mass: 22768.242 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: synthetic gene (NCBI-GeneID:890139) codon optimized for Escherichia coli Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: J99 Gene: jhp_0755, synthetic gene codon optimized for Escherichia coli Plasmid: pET15bmod / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: Q9ZL26
Mass: 18.015 Da / Num. of mol.: 394 / Source method: isolated from a natural source / Formula: H2O
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Details
Nonpolymer details
1. THE COORDINATION SPHERES PROVIDED AUTOMATICALLY AS REMARK 620 HAVE BEEN SKIPPED UPON AUTHOR'S ...1. THE COORDINATION SPHERES PROVIDED AUTOMATICALLY AS REMARK 620 HAVE BEEN SKIPPED UPON AUTHOR'S REQUEST BECAUSE THESE RECORDS MAKE A FALSE IMPRESSION THAT THE SODIUM IS OCTA-COORDINATED. THE CORRECT RECORDS ARE PROVIDED IN THE MMCIF FILE IN CATEGORY _DATABASE_PDB_REMARK. 2. THE LINK RECORDS THAT INVOLVE ZN AND NA IONS HAVE BEEN REMOVED UPON AUTHOR'S REQUEST.
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.5 Å3/Da / Density % sol: 50.77 %
Crystal grow
Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M MES/Sodium hydroxide pH 6.5, 0.1 M Sodium chloride, 0.1 M Lithium sulfate, 30 % PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Type: MARRESEARCH / Detector: CCD / Date: Aug 8, 2008
Radiation
Monochromator: KMC-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97982 Å / Relative weight: 1
Reflection
Resolution: 1.75→20 Å / Num. all: 51564 / Num. obs: 51564 / % possible obs: 96.8 % / Redundancy: 3.99 % / Biso Wilson estimate: 22.6 Å2 / Rsym value: 0.066 / Net I/σ(I): 13.52
Reflection shell
Resolution: 1.75→1.8 Å / Redundancy: 3.95 % / Mean I/σ(I) obs: 4.48 / Num. unique all: 3874 / Rsym value: 0.4 / % possible all: 99.1
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Processing
Software
Name
Version
Classification
MxCuBE
datacollection
SHELXCD
phasing
SHELXD
phasing
SHELXE
modelbuilding
ARP/wARP
modelbuilding
REFMAC
5.2.0019
refinement
XDS
datareduction
XSCALE
datascaling
Refinement
Method to determine structure: SAD / Resolution: 1.75→19.71 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: CNS HAS BEEN USED FOR DNA REFINEMENT. NO SUGAR PUCKER CONSTRAINTS HAVE BEEN APPLIED. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TLS REFINEMENT HAS BEEN USED.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.20533
2654
5.1 %
RANDOM
Rwork
0.18084
-
-
-
all
0.18212
51564
-
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obs
0.18212
51564
96.86 %
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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: MASK
Displacement parameters
Biso mean: 21.338 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.88 Å2
0.44 Å2
0 Å2
2-
-
0.88 Å2
0 Å2
3-
-
-
-1.31 Å2
Refinement step
Cycle: LAST / Resolution: 1.75→19.71 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2974
363
20
394
3751
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.01
0.022
3935
X-RAY DIFFRACTION
r_bond_other_d
0
0.02
2541
X-RAY DIFFRACTION
r_angle_refined_deg
1.224
2.199
5453
X-RAY DIFFRACTION
r_angle_other_deg
3.917
3
6247
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.633
5
395
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
35.996
24.722
144
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.154
15
598
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
20.812
15
21
X-RAY DIFFRACTION
r_chiral_restr
0.077
0.2
600
X-RAY DIFFRACTION
r_gen_planes_refined
0.009
0.02
3866
X-RAY DIFFRACTION
r_gen_planes_other
0.007
0.02
677
X-RAY DIFFRACTION
r_nbd_refined
0.205
0.2
618
X-RAY DIFFRACTION
r_nbd_other
0.238
0.2
2291
X-RAY DIFFRACTION
r_nbtor_refined
0.187
0.2
1754
X-RAY DIFFRACTION
r_nbtor_other
0.106
0.2
1565
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.135
0.2
307
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
0.111
0.2
9
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.296
0.2
9
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.304
0.2
57
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.157
0.2
14
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
0.066
0.2
1
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
0.687
1.5
1925
X-RAY DIFFRACTION
r_mcbond_other
0
1.5
790
X-RAY DIFFRACTION
r_mcangle_it
1.263
2
3130
X-RAY DIFFRACTION
r_scbond_it
1.745
3
2010
X-RAY DIFFRACTION
r_scangle_it
2.662
4.5
2323
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 1.75→1.795 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.251
185
-
Rwork
0.234
3657
-
obs
-
3842
99.05 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
1.1687
-0.4824
-0.1777
2.49
-0.5355
2.0544
0.0228
0.0612
-0.0263
-0.1372
0.0107
-0.1222
0.0872
0.1593
-0.0335
-0.0427
0.018
-0.0071
-0.0691
-0.0164
-0.0135
2.654
16.229
114.446
2
0.8766
-0.5012
-0.8485
0.7494
0.9899
1.3717
-0.1307
-0.1114
-0.0568
0.1059
0.0933
-0.0105
0.2383
0.218
0.0374
0.0142
0.0268
-0.0139
-0.0772
0.0029
-0.0296
-8.541
15.134
134.469
3
0.2477
-0.3117
-0.1504
0.4091
0.3304
1.2717
0.1197
-0.2271
0.1738
-0.0526
0.0999
-0.0701
-0.2383
0.2488
-0.2195
0.0257
-0.0418
0.0345
0.0098
-0.0703
-0.0216
-9.917
35.179
144.17
4
2.7444
0.5645
0.9957
0.7666
0.3846
2.1184
-0.0378
-0.189
0.1169
0.1184
-0.0236
0.0477
-0.0724
-0.1676
0.0614
0.0145
0.0158
0.0055
0.008
-0.0193
-0.0241
-34.884
41.309
164.546
5
1.4182
-0.2256
-1.4575
0.6018
0.2699
1.5005
0.0776
0.064
-0.026
0.0113
-0.1184
0.0639
-0.0669
-0.3362
0.0408
-0.003
0.0127
-0.0082
0.0149
-0.0173
-0.0169
-31.574
29.973
144.372
6
0.6785
0.006
-0.2728
0.347
0.4535
1.4156
0.2055
-0.0358
0.1469
-0.1489
-0.0382
-0.1251
-0.3543
-0.0334
-0.1673
0.0804
0.0089
0.06
-0.0898
-0.0166
-0.0263
-13.212
36.944
134.113
7
1.071
-0.5818
-0.588
0.5697
0.3853
1.9216
-0.033
-0.045
-0.1168
0.064
-0.0031
0.0663
0.0439
-0.094
0.0361
-0.0422
-0.0029
0.0105
-0.0923
-0.0145
-0.0673
-19.387
23.525
139.532
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
2 - 54
2
X-RAY DIFFRACTION
2
A
55 - 113
3
X-RAY DIFFRACTION
3
A
134 - 188
4
X-RAY DIFFRACTION
4
B
2 - 54
5
X-RAY DIFFRACTION
5
B
55 - 113
6
X-RAY DIFFRACTION
6
B
134 - 188
7
X-RAY DIFFRACTION
7
C
-4 - 4
8
X-RAY DIFFRACTION
7
D
-4 - 4
+
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