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- PDB-4b56: Structure of ectonucleotide pyrophosphatase-phosphodiesterase-1 (NPP1) -

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Entry
Database: PDB / ID: 4b56
TitleStructure of ectonucleotide pyrophosphatase-phosphodiesterase-1 (NPP1)
ComponentsECTONUCLEOTIDE PYROPHOSPHATASE/PHOSPHODIESTERASE FAMILY MEMBER 1
KeywordsHYDROLASE
Function / homology
Function and homology information


microglial cell migration / cellular response to sodium phosphate / Vitamin B2 (riboflavin) metabolism / articular cartilage development / response to platelet-derived growth factor / ligamentous ossification / cyclic-GMP-AMP hydrolase activity / negative regulation of hh target transcription factor activity / response to vitamin B6 / organic phosphonate metabolic process ...microglial cell migration / cellular response to sodium phosphate / Vitamin B2 (riboflavin) metabolism / articular cartilage development / response to platelet-derived growth factor / ligamentous ossification / cyclic-GMP-AMP hydrolase activity / negative regulation of hh target transcription factor activity / response to vitamin B6 / organic phosphonate metabolic process / inorganic diphosphate transport / post-embryonic forelimb morphogenesis / GTP diphosphatase activity / tooth mineralization / hematopoietic stem cell migration to bone marrow / UTP diphosphatase activity / leukocyte activation involved in inflammatory response / dinucleotide phosphatase activity / coenzyme A diphosphatase activity / bone growth / coenzyme A catabolic process / biomineral tissue development / vascular associated smooth muscle cell migration / sensory perception of temperature stimulus / phosphodiesterase I / nucleotide diphosphatase / response to Gram-positive bacterium / inhibition of non-skeletal tissue mineralization / pyrophosphatase activity / magnesium ion homeostasis / endochondral bone morphogenesis / diphosphate metabolic process / bone trabecula formation / vascular associated smooth muscle cell proliferation / nucleoside triphosphate diphosphatase activity / vitamin D3 metabolic process / cementum mineralization / central nervous system myelination / mucus secretion / bone mineralization involved in bone maturation / response to sodium phosphate / ATP diphosphatase activity / sensory perception of mechanical stimulus / negative regulation of bone mineralization / phosphate ion homeostasis / B-1 B cell homeostasis / artery development / collagen-activated signaling pathway / endochondral ossification / apoptotic process involved in development / microglia differentiation / bone remodeling / phosphoric diester hydrolase activity / inflammatory response to antigenic stimulus / cellular homeostasis / hormone metabolic process / plasma cell differentiation / oligodendrocyte apoptotic process / cartilage development / negative regulation of ossification / phosphodiesterase I activity / odontogenesis / adult walking behavior / axon regeneration / scavenger receptor activity / fat pad development / middle ear morphogenesis / aorta development / smoothened signaling pathway / protein poly-ADP-ribosylation / skin development / muscle cell cellular homeostasis / defense response to protozoan / spinal cord development / negative regulation of fat cell differentiation / D-glucose import / bone mineralization / fat cell differentiation / response to dietary excess / phosphatase activity / polysaccharide binding / response to magnesium ion / macrophage differentiation / T cell differentiation / 3',5'-cyclic-AMP phosphodiesterase activity / fibroblast growth factor receptor signaling pathway / adipose tissue development / bone resorption / vasculogenesis / ATP metabolic process / calcium ion homeostasis / ossification / osteoclast differentiation / morphogenesis of an epithelium / adult locomotory behavior / glycolytic process / determination of adult lifespan / mitochondrion organization / kidney development / establishment of localization in cell
Similarity search - Function
Gyrase A; domain 2 - #180 / Extracellular Endonuclease; Chain A / Extracellular Endonuclease, subunit A / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Somatomedin B domain, chordata / Somatomedin B -like domains / Somatomedin B domain / Somatomedin B-like domain superfamily / Somatomedin B domain ...Gyrase A; domain 2 - #180 / Extracellular Endonuclease; Chain A / Extracellular Endonuclease, subunit A / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Somatomedin B domain, chordata / Somatomedin B -like domains / Somatomedin B domain / Somatomedin B-like domain superfamily / Somatomedin B domain / Somatomedin B domain (SMB) signature. / Somatomedin B (SMB) domain profile. / Type I phosphodiesterase/nucleotide pyrophosphatase/phosphate transferase / Type I phosphodiesterase / nucleotide pyrophosphatase / Extracellular Endonuclease, subunit A / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease superfamily / His-Me finger superfamily / Alkaline-phosphatase-like, core domain superfamily / Gyrase A; domain 2 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Ectonucleotide pyrophosphatase/phosphodiesterase family member 1
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsJansen, S. / Perrakis, A. / Ulens, C. / Winkler, C. / Andries, M. / Joosten, R.P. / Van Acker, M. / Luyten, F.P. / Moolenaar, W.H. / Bollen, M.
CitationJournal: Structure / Year: 2012
Title: Structure of Npp1, an Ectonucleotide Pyrophosphatase/Phosphodiesterase Involved in Tissue Calcification.
Authors: Jansen, S. / Perrakis, A. / Ulens, C. / Winkler, C. / Andries, M. / Joosten, R.P. / Van Acker, M. / Luyten, F.P. / Moolenaar, W.H. / Bollen, M.
History
DepositionAug 2, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 19, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2012Group: Database references
Revision 1.2Nov 21, 2012Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_label_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.conn_type_id / _struct_conn.id / _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 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ECTONUCLEOTIDE PYROPHOSPHATASE/PHOSPHODIESTERASE FAMILY MEMBER 1
B: ECTONUCLEOTIDE PYROPHOSPHATASE/PHOSPHODIESTERASE FAMILY MEMBER 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,77718
Polymers188,5282
Non-polymers4,24916
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7420 Å2
ΔGint-101.3 kcal/mol
Surface area64130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.385, 105.412, 245.258
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: _ / Auth seq-ID: 169 - 902 / Label seq-ID: 83 - 816

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ECTONUCLEOTIDE PYROPHOSPHATASE/PHOSPHODIESTERASE FAMILY MEMBER 1 / ECTONUCLEOTIDE PYROPHOSPHATASE-PHOSPHODIESTERASE-1 / E-NPP 1 / LYMPHOCYTE ANTIGEN 41 / LY-41 / ...ECTONUCLEOTIDE PYROPHOSPHATASE-PHOSPHODIESTERASE-1 / E-NPP 1 / LYMPHOCYTE ANTIGEN 41 / LY-41 / PHOSPHODIESTERASE I/NUCLEOTIDE PYROPHOSPHATASE 1 / PLASMA-CELL MEMBRANE GLYCOPROTEIN PC-1 / ALKALINE PHOSPHODIESTERASE I / NUCLEOTIDE PYROPHOSPHATASE / NPPASE


Mass: 94264.055 Da / Num. of mol.: 2 / Fragment: RESIDUES 87-906
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell line (production host): HEK293S GNTI / Production host: HOMO SAPIENS (human)
References: UniProt: P06802, phosphodiesterase I, nucleotide diphosphatase

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Sugars , 4 types, 8 molecules

#2: 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.: 2
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
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-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.: 4
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 , 3 types, 8 molecules

#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4

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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: 3.54 Å3/Da / Density % sol: 65.3 % / Description: NONE
Crystal growpH: 8
Details: 100 NL PROTEIN SOLUTION WITH 100 NL 10% PROPANOL, 0.1 M IMIDAZOLE AT PH 8.0 AND 3% 1,4-DIOXANE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 3→48.47 Å / Num. obs: 51597 / % possible obs: 99.7 % / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 110 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.1
Reflection shellResolution: 3→3.16 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.1 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XRG

2xrg


Resolution: 3→48.47 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.94 / SU B: 38.967 / SU ML: 0.3 / Cross valid method: THROUGHOUT / ESU R: 4.29 / ESU R Free: 0.356 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2335 2763 5.13 %RANDOM
Rwork0.2002 ---
obs0.202 51597 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 116.185 Å2
Baniso -1Baniso -2Baniso -3
1-3.484 Å20 Å20 Å2
2--7.41 Å20 Å2
3----10.894 Å2
Refinement stepCycle: LAST / Resolution: 3→48.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12573 0 261 0 12834
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01913232
X-RAY DIFFRACTIONr_bond_other_d0.0030.0212205
X-RAY DIFFRACTIONr_angle_refined_deg1.2711.98418020
X-RAY DIFFRACTIONr_angle_other_deg0.8683.00328128
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.23651551
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.54723.99614
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.307152174
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8611566
X-RAY DIFFRACTIONr_chiral_restr0.070.21967
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02114635
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023043
X-RAY DIFFRACTIONr_nbd_refined0.210.22967
X-RAY DIFFRACTIONr_nbd_other0.1830.275
X-RAY DIFFRACTIONr_nbtor_refined0.1830.26413
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2288
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1080.212
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1830.275
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.080.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7347.14313232
X-RAY DIFFRACTIONr_mcbond_other0.3557.1512205
X-RAY DIFFRACTIONr_mcangle_it2.88710.69618020
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.4621.3731660
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.14570.5823385
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 45590 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 192 -
Rwork0.344 3773 -
obs--99.899 %
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)
10.87590.11990.14482.7803-0.94961.9222-0.0274-0.0343-0.03830.02470.05270.1443-0.1171-0.2412-0.02530.04520.01960.0170.0349-0.02890.432636.68634.133582.8933
21.95750.59280.67281.45010.24642.12150.023-0.0554-0.16670.15260.0599-0.27050.36560.8674-0.0830.36780.19980.05510.4231-0.02930.508675.68447.3834101.2728
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A88 - 2032
2X-RAY DIFFRACTION2B88 - 2032

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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