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- PDB-4dl1: Crystal Structure of human Myeloperoxidase with covalent thioxant... -

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Basic information

Entry
Database: PDB / ID: 4dl1
TitleCrystal Structure of human Myeloperoxidase with covalent thioxanthine analog
Components(Myeloperoxidase ...) x 2
KeywordsOXIDOREDUCTASE / Heme-dependent peroxidase
Function / homology
Function and homology information


myeloperoxidase / hypochlorous acid biosynthetic process / Events associated with phagocytolytic activity of PMN cells / phagocytic vesicle lumen / response to gold nanoparticle / response to yeast / respiratory burst involved in defense response / low-density lipoprotein particle remodeling / azurophil granule / response to food ...myeloperoxidase / hypochlorous acid biosynthetic process / Events associated with phagocytolytic activity of PMN cells / phagocytic vesicle lumen / response to gold nanoparticle / response to yeast / respiratory burst involved in defense response / low-density lipoprotein particle remodeling / azurophil granule / response to food / defense response to fungus / response to mechanical stimulus / removal of superoxide radicals / secretory granule / hydrogen peroxide catabolic process / peroxidase activity / defense response / azurophil granule lumen / heparin binding / response to oxidative stress / response to lipopolysaccharide / lysosome / defense response to bacterium / intracellular membrane-bounded organelle / heme binding / Neutrophil degranulation / chromatin binding / negative regulation of apoptotic process / extracellular space / extracellular exosome / extracellular region / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
Myeloperoxidase, subunit C / Haem peroxidase domain superfamily, animal type / Haem peroxidase, animal-type / Haem peroxidase domain superfamily, animal type / Animal haem peroxidase / Animal heme peroxidase superfamily profile. / Peroxidases proximal heme-ligand signature. / Haem peroxidase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-0KY / PROTOPORPHYRIN IX CONTAINING FE / Myeloperoxidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsVajdos, F. / Varghese, A.
CitationJournal: Biochemistry / Year: 2012
Title: Deconstruction of activity-dependent covalent modification of heme in human neutrophil myeloperoxidase by multistage mass spectrometry (MS(4)).
Authors: Geoghegan, K.F. / Varghese, A.H. / Feng, X. / Bessire, A.J. / Conboy, J.J. / Ruggeri, R.B. / Ahn, K. / Spath, S.N. / Filippov, S.V. / Conrad, S.J. / Carpino, P.A. / Guimaraes, C.R. / Vajdos, F.F.
History
DepositionFeb 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1May 9, 2012Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Dec 25, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myeloperoxidase light chain
C: Myeloperoxidase heavy chain
B: Myeloperoxidase light chain
D: Myeloperoxidase heavy chain
E: Myeloperoxidase light chain
G: Myeloperoxidase heavy chain
F: Myeloperoxidase light chain
H: Myeloperoxidase heavy chain
I: Myeloperoxidase light chain
K: Myeloperoxidase heavy chain
J: Myeloperoxidase light chain
L: Myeloperoxidase heavy chain
M: Myeloperoxidase light chain
O: Myeloperoxidase heavy chain
N: Myeloperoxidase light chain
P: Myeloperoxidase heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)541,35672
Polymers521,10016
Non-polymers20,25556
Water45,3982520
1
A: Myeloperoxidase light chain
C: Myeloperoxidase heavy chain
B: Myeloperoxidase light chain
D: Myeloperoxidase heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,16618
Polymers130,2754
Non-polymers4,89114
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Myeloperoxidase light chain
G: Myeloperoxidase heavy chain
F: Myeloperoxidase light chain
H: Myeloperoxidase heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,16618
Polymers130,2754
Non-polymers4,89114
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: Myeloperoxidase light chain
K: Myeloperoxidase heavy chain
J: Myeloperoxidase light chain
L: Myeloperoxidase heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,16618
Polymers130,2754
Non-polymers4,89114
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
M: Myeloperoxidase light chain
O: Myeloperoxidase heavy chain
N: Myeloperoxidase light chain
P: Myeloperoxidase heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,85618
Polymers130,2754
Non-polymers5,58114
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Myeloperoxidase light chain
C: Myeloperoxidase heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5839
Polymers65,1382
Non-polymers2,4467
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14680 Å2
ΔGint-75 kcal/mol
Surface area22860 Å2
MethodPISA
6
B: Myeloperoxidase light chain
D: Myeloperoxidase heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5839
Polymers65,1382
Non-polymers2,4467
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14740 Å2
ΔGint-73 kcal/mol
Surface area22850 Å2
MethodPISA
7
E: Myeloperoxidase light chain
G: Myeloperoxidase heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5839
Polymers65,1382
Non-polymers2,4467
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14430 Å2
ΔGint-73 kcal/mol
Surface area22910 Å2
MethodPISA
8
F: Myeloperoxidase light chain
H: Myeloperoxidase heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5839
Polymers65,1382
Non-polymers2,4467
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14450 Å2
ΔGint-70 kcal/mol
Surface area22970 Å2
MethodPISA
9
I: Myeloperoxidase light chain
K: Myeloperoxidase heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5839
Polymers65,1382
Non-polymers2,4467
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14780 Å2
ΔGint-73 kcal/mol
Surface area22730 Å2
MethodPISA
10
J: Myeloperoxidase light chain
L: Myeloperoxidase heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5839
Polymers65,1382
Non-polymers2,4467
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14780 Å2
ΔGint-75 kcal/mol
Surface area22630 Å2
MethodPISA
11
M: Myeloperoxidase light chain
O: Myeloperoxidase heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5839
Polymers65,1382
Non-polymers2,4467
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14350 Å2
ΔGint-71 kcal/mol
Surface area23050 Å2
MethodPISA
12
N: Myeloperoxidase light chain
P: Myeloperoxidase heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2739
Polymers65,1382
Non-polymers3,1357
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15250 Å2
ΔGint-59 kcal/mol
Surface area23310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.829, 242.636, 151.505
Angle α, β, γ (deg.)90.00, 91.19, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31E
41F
51I
61J
71M
81N
12C
22D
32G
42H
52K
62L
72O
82P

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A1 - 605
2116B1 - 605
3116E1 - 605
4116F1 - 605
5116I1 - 605
6116J1 - 605
7116M1 - 605
8116N1 - 605
1126C113 - 578
2126D113 - 578
3126G113 - 578
4126H113 - 578
5126K113 - 578
6126L113 - 578
7126O113 - 578
8126P113 - 578

NCS ensembles :
ID
1
2

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Components

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Myeloperoxidase ... , 2 types, 16 molecules ABEFIJMNCDGHKLOP

#1: Protein
Myeloperoxidase light chain


Mass: 11903.343 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Details: blood / Source: (natural) Homo sapiens (human) / References: UniProt: P05164, myeloperoxidase
#2: Protein
Myeloperoxidase heavy chain


Mass: 53234.191 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P05164, myeloperoxidase

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Sugars , 3 types, 24 molecules

#3: Polysaccharide
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#8: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 2552 molecules

#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-0KY / 3-[(2R)-2-ethoxypropyl]-2-thioxo-1,2,3,9-tetrahydro-6H-purin-6-one


Mass: 254.309 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H14N4O2S
#7: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#9: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2520 / 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: 2.25 Å3/Da / Density % sol: 45.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.5
Details: 27% PEG 3350, 0.25 M CaCl2, betaine HCl, pH 5.5, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: PILATUS 6M / Detector: PIXEL ARRAY DETECTOR / Date: Dec 3, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→242.636 Å / Num. all: 335809 / Num. obs: 335809 / % possible obs: 93.3 % / Redundancy: 3.1 % / Rsym value: 0.091 / Net I/σ(I): 7.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.9-21.70.4931.60.493167.4
2-2.122.60.4061.90.406192.9
2.12-2.273.30.3142.50.314198.6
2.27-2.453.40.2193.50.219198.9
2.45-2.693.40.15450.154199
2.69-33.50.1086.90.108198.9
3-3.473.30.0759.30.075198.9
3.47-4.253.50.05711.70.057198.2
4.25-6.013.30.05311.40.053198.4
6.01-242.6363.30.0519.70.051196.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 38.87 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å128.49 Å
Translation2.5 Å128.49 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→128.49 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.912 / Occupancy max: 1 / Occupancy min: 1 / SU B: 11.978 / SU ML: 0.148 / SU R Cruickshank DPI: 0.2325 / Cross valid method: THROUGHOUT / ESU R: 0.222 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24617 15173 5 %RANDOM
Rwork0.19045 ---
obs0.19327 286325 97.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.802 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å20.33 Å2
2---0.52 Å20 Å2
3---0.75 Å2
Refinement stepCycle: LAST / Resolution: 2→128.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms36531 0 1335 2520 40386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02239030
X-RAY DIFFRACTIONr_bond_other_d0.0010.0227347
X-RAY DIFFRACTIONr_angle_refined_deg1.1722.02353111
X-RAY DIFFRACTIONr_angle_other_deg0.734365714
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9554545
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.39722.8991859
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.882156257
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.50215432
X-RAY DIFFRACTIONr_chiral_restr0.1760.25779
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02142470
X-RAY DIFFRACTIONr_gen_planes_other0.0010.027976
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1891.522944
X-RAY DIFFRACTIONr_mcbond_other0.3961.59004
X-RAY DIFFRACTIONr_mcangle_it1.799237124
X-RAY DIFFRACTIONr_scbond_it3.082316086
X-RAY DIFFRACTIONr_scangle_it4.2384.515985
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1438LOOSE POSITIONAL0.385
12B1438LOOSE POSITIONAL0.345
13E1438LOOSE POSITIONAL0.45
14F1438LOOSE POSITIONAL0.45
15I1438LOOSE POSITIONAL0.465
16J1438LOOSE POSITIONAL0.435
17M1438LOOSE POSITIONAL0.415
18N1438LOOSE POSITIONAL0.395
11A1438LOOSE THERMAL2.8610
12B1438LOOSE THERMAL2.1810
13E1438LOOSE THERMAL2.3510
14F1438LOOSE THERMAL2.9410
15I1438LOOSE THERMAL2.3110
16J1438LOOSE THERMAL2.1210
17M1438LOOSE THERMAL2.0410
18N1438LOOSE THERMAL2.810
21C6424LOOSE POSITIONAL0.435
22D6424LOOSE POSITIONAL0.395
23G6424LOOSE POSITIONAL0.415
24H6424LOOSE POSITIONAL0.395
25K6424LOOSE POSITIONAL0.45
26L6424LOOSE POSITIONAL0.425
27O6424LOOSE POSITIONAL0.45
28P6424LOOSE POSITIONAL0.415
21C6424LOOSE THERMAL2.4610
22D6424LOOSE THERMAL2.1610
23G6424LOOSE THERMAL2.3210
24H6424LOOSE THERMAL2.3210
25K6424LOOSE THERMAL2.410
26L6424LOOSE THERMAL2.1910
27O6424LOOSE THERMAL2.1210
28P6424LOOSE THERMAL2.4110
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 1008 -
Rwork0.258 19262 -
obs--88.92 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.8865-0.04670.36771.3576-0.06591.13460.0219-0.0166-0.0168-0.02340.00620.05360.0373-0.0116-0.02810.0162-0.0051-0.00120.11260.00620.013110.742-16.50243.89
21.00250.19590.49480.99490.20220.89050.00050.07790.0408-0.1469-0.01130.1015-0.0195-0.00050.01090.0758-0.0061-0.02160.09310.00970.0135.375-15.30734.498
31.5089-0.07590.3621.52670.22340.9731-0.0079-0.051-0.20130.06530.02450.050.16150.0078-0.01650.08940.0304-0.00520.12020.00590.056724.696-42.22260.505
41.1359-0.2190.55181.03730.10131.0505-0.0007-0.1094-0.18520.12430.0608-0.04910.14680.0359-0.060.10410.0456-0.03080.11250.00360.091933.254-43.47767.265
51.3944-0.0735-0.47521.33580.30551.49050.0577-0.1860.0450.02770.05850.0383-0.08890.0232-0.11620.0362-0.03620.01710.1812-0.04220.0504-21.07717.08770.935
61.4168-0.2191-0.43351.06030.27221.1538-0.012-0.4118-0.01540.19440.04640.0889-0.006-0.0128-0.03450.117-0.01320.04270.2797-0.02010.0344-26.40116.08680.372
71.50810.2035-0.00231.5050.33980.7629-0.04940.0140.343-0.0051-0.01490.1488-0.1435-0.00020.06440.1699-0.05560.03460.1404-0.02110.1692-7.34842.48553.657
81.2820.1423-0.54891.11840.09910.8658-0.0040.11660.3179-0.13070.0013-0.0815-0.16660.03020.00270.184-0.07810.02930.1507-0.02030.22641.17643.62946.838
91.07610.43080.06991.4122-0.13121.25490.0978-0.00160.0960.0483-0.03660.1828-0.0226-0.0923-0.06110.0954-0.0063-0.02540.1041-0.00780.0833-17.88516.094-7.023
101.23850.1858-0.10331.33630.13490.97970.1529-0.18180.08040.2589-0.11840.2639-0.0144-0.1337-0.03460.1728-0.04420.02280.1286-0.02120.0933-23.19214.9132.403
111.3722-0.0227-0.38840.97780.00281.0550.02360.05230.1828-0.0460.02030.145-0.1382-0.0611-0.04390.1579-0.0139-0.03720.11840.01170.116-4.18341.814-23.839
120.80210.0688-0.4180.87820.12021.00710.04060.10530.1397-0.1020.0131-0.0121-0.14090.0242-0.05360.1596-0.0298-0.01730.11960.02230.13364.32943.087-30.65
131.72060.17420.96920.73990.28261.9425-0.03210.12550.0501-0.0311-0.0090.0743-0.01790.03620.04120.08890.031-0.08910.1234-0.01860.132913.77-17.814-33.746
141.47390.25291.0460.87060.20391.5849-0.09480.21260.1487-0.1113-0.03640.0832-0.09510.01690.13130.14990.0192-0.09370.1682-0.0150.12778.541-17.04-43.259
151.7858-0.29120.71740.6615-0.31751.58670.1066-0.0025-0.2915-0.0727-0.00940.20450.2805-0.1515-0.09710.2065-0.0126-0.0920.1305-0.01320.17926.493-42.898-15.275
161.1195-0.32630.9440.9676-0.06441.86450.0876-0.0647-0.19820.0423-0.03780.08740.2773-0.0922-0.04990.1892-0.0005-0.07880.0966-0.00490.190834.932-44.041-8.346
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 104
2X-RAY DIFFRACTION1A1601 - 1602
3X-RAY DIFFRACTION1C601
4X-RAY DIFFRACTION1A1701 - 1756
5X-RAY DIFFRACTION1B301
6X-RAY DIFFRACTION1C701 - 702
7X-RAY DIFFRACTION2C113 - 577
8X-RAY DIFFRACTION2C602 - 610
9X-RAY DIFFRACTION2A1757 - 1759
10X-RAY DIFFRACTION2C703 - 914
11X-RAY DIFFRACTION2D701
12X-RAY DIFFRACTION2F301
13X-RAY DIFFRACTION3B1 - 104
14X-RAY DIFFRACTION3B201 - 203
15X-RAY DIFFRACTION3B302 - 341
16X-RAY DIFFRACTION3D702
17X-RAY DIFFRACTION4D113 - 578
18X-RAY DIFFRACTION4D601 - 609
19X-RAY DIFFRACTION4B342 - 347
20X-RAY DIFFRACTION4D703 - 873
21X-RAY DIFFRACTION5E1 - 104
22X-RAY DIFFRACTION5E1601 - 1602
23X-RAY DIFFRACTION5E1701 - 1741
24X-RAY DIFFRACTION5F302 - 303
25X-RAY DIFFRACTION5G701
26X-RAY DIFFRACTION5H1701
27X-RAY DIFFRACTION6G113 - 577
28X-RAY DIFFRACTION6G601 - 610
29X-RAY DIFFRACTION6C915
30X-RAY DIFFRACTION6G702 - 845
31X-RAY DIFFRACTION7F1 - 104
32X-RAY DIFFRACTION7F201 - 202
33X-RAY DIFFRACTION7C916
34X-RAY DIFFRACTION7E1742
35X-RAY DIFFRACTION7F304 - 350
36X-RAY DIFFRACTION7G846
37X-RAY DIFFRACTION7H1702 - 1703
38X-RAY DIFFRACTION8H113 - 578
39X-RAY DIFFRACTION8H601 - 610
40X-RAY DIFFRACTION8F351 - 355
41X-RAY DIFFRACTION8G847 - 849
42X-RAY DIFFRACTION8H1704 - 1814
43X-RAY DIFFRACTION9I1 - 104
44X-RAY DIFFRACTION9I1601 - 1603
45X-RAY DIFFRACTION9I1701 - 1747
46X-RAY DIFFRACTION9J301
47X-RAY DIFFRACTION9K701
48X-RAY DIFFRACTION10K113 - 577
49X-RAY DIFFRACTION10K601 - 609
50X-RAY DIFFRACTION10I1748 - 1751
51X-RAY DIFFRACTION10K702 - 832
52X-RAY DIFFRACTION10L701
53X-RAY DIFFRACTION11J1 - 104
54X-RAY DIFFRACTION11J201 - 203
55X-RAY DIFFRACTION11J302 - 350
56X-RAY DIFFRACTION11L702 - 703
57X-RAY DIFFRACTION12L113 - 578
58X-RAY DIFFRACTION12L601 - 609
59X-RAY DIFFRACTION12J351 - 352
60X-RAY DIFFRACTION12K833
61X-RAY DIFFRACTION12L704 - 859
62X-RAY DIFFRACTION13M1 - 104
63X-RAY DIFFRACTION13M1601 - 1602
64X-RAY DIFFRACTION13M1701 - 1741
65X-RAY DIFFRACTION13O701
66X-RAY DIFFRACTION14O113 - 578
67X-RAY DIFFRACTION14O601 - 610
68X-RAY DIFFRACTION14M1742 - 1743
69X-RAY DIFFRACTION14O702 - 830
70X-RAY DIFFRACTION14P701 - 702
71X-RAY DIFFRACTION15N1 - 104
72X-RAY DIFFRACTION15N201 - 202
73X-RAY DIFFRACTION15P601
74X-RAY DIFFRACTION15N301 - 339
75X-RAY DIFFRACTION15O831
76X-RAY DIFFRACTION15P703 - 704
77X-RAY DIFFRACTION16P113 - 578
78X-RAY DIFFRACTION16P602 - 614
79X-RAY DIFFRACTION16C917
80X-RAY DIFFRACTION16N340 - 341
81X-RAY DIFFRACTION16P705 - 840

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