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Basic information

Entry
Database: PDB / ID: 2w0d
TitleDoes a Fast Nuclear Magnetic Resonance Spectroscopy- and X-Ray Crystallography Hybrid Approach Provide Reliable Structural Information of Ligand-Protein Complexes? A Case Study of Metalloproteinases.
ComponentsMACROPHAGE METALLOELASTASE
KeywordsHYDROLASE / GLYCOPROTEIN / METAL-BINDING / METALLOPROTEASE / SECRETED / HYDROXAMATE / EXTRACELLULAR MATRIX / COPD / MMP-12 / ZYMOGEN
Function / homology
Function and homology information


macrophage elastase / negative regulation of endothelial cell-matrix adhesion via fibronectin / bronchiole development / positive regulation of epithelial cell proliferation involved in wound healing / elastin catabolic process / regulation of defense response to virus by host / positive regulation of type I interferon-mediated signaling pathway / wound healing, spreading of epidermal cells / negative regulation of type I interferon-mediated signaling pathway / lung alveolus development ...macrophage elastase / negative regulation of endothelial cell-matrix adhesion via fibronectin / bronchiole development / positive regulation of epithelial cell proliferation involved in wound healing / elastin catabolic process / regulation of defense response to virus by host / positive regulation of type I interferon-mediated signaling pathway / wound healing, spreading of epidermal cells / negative regulation of type I interferon-mediated signaling pathway / lung alveolus development / response to amyloid-beta / Collagen degradation / positive regulation of interferon-alpha production / collagen catabolic process / extracellular matrix disassembly / core promoter sequence-specific DNA binding / collagen binding / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / metalloendopeptidase activity / cellular response to virus / protein import into nucleus / endopeptidase activity / sequence-specific DNA binding / serine-type endopeptidase activity / calcium ion binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / proteolysis / extracellular space / extracellular region / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidoglycan binding-like / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Putative peptidoglycan binding domain ...Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidoglycan binding-like / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Putative peptidoglycan binding domain / Hemopexin repeat profile. / Hemopexin-like repeats. / Peptidase M10A / Peptidase M10A, catalytic domain / Peptidase M10, metallopeptidase / Matrixin / PGBD-like superfamily / Peptidase, metallopeptidase / Zinc-dependent metalloprotease / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Chem-CGS / Macrophage metalloelastase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsIsaksson, J. / Nystrom, S. / Derbyshire, D.J. / Wallberg, H. / Agback, T. / Kovacs, H. / Bertini, I. / Felli, I.C.
CitationJournal: J.Med.Chem. / Year: 2009
Title: Does a Fast Nuclear Magnetic Resonance Spectroscopy- and X-Ray Crystallography Hybrid Approach Provide Reliable Structural Information of Ligand-Protein Complexes? a Case Study of Metalloproteinases.
Authors: Isaksson, J. / Nystrom, S. / Derbyshire, D.J. / Wallberg, H. / Agback, T. / Kovacs, H. / Bertini, I. / Felli, I.C.
History
DepositionAug 13, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2Dec 28, 2011Group: Other
Revision 1.3May 22, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval ..._exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.4May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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.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_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 / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MACROPHAGE METALLOELASTASE
B: MACROPHAGE METALLOELASTASE
C: MACROPHAGE METALLOELASTASE
D: MACROPHAGE METALLOELASTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,33840
Polymers73,1224
Non-polymers3,21636
Water12,304683
1
A: MACROPHAGE METALLOELASTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,16811
Polymers18,2801
Non-polymers88710
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MACROPHAGE METALLOELASTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9257
Polymers18,2801
Non-polymers6456
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: MACROPHAGE METALLOELASTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,14411
Polymers18,2801
Non-polymers86310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: MACROPHAGE METALLOELASTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,10111
Polymers18,2801
Non-polymers82110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.160, 99.939, 79.423
Angle α, β, γ (deg.)90.00, 96.59, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
42D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PROPROHISHIS4AA107 - 1123 - 8
211PROPROHISHIS4BB107 - 1123 - 8
311PROPROHISHIS4CC107 - 1123 - 8
411PROPROHISHIS4DD107 - 1123 - 8
121TYRTYRTYRTYR5AA1139
221TYRTYRTYRTYR5BB1139
321TYRTYRTYRTYR5CC1139
421TYRTYRTYRTYR5DD1139
131ILEILEASNASN4AA114 - 12610 - 22
231ILEILEASNASN4BB114 - 12610 - 22
331ILEILEASNASN4CC114 - 12610 - 22
431ILEILEASNASN4DD114 - 12610 - 22
141ARGARGARGARG5AA12723
241ARGARGARGARG5BB12723
341ARGARGARGARG5CC12723
441ARGARGARGARG5DD12723
151GLUGLUILEILE2AA128 - 15224 - 48
251GLUGLUILEILE2BB128 - 15224 - 48
351GLUGLUILEILE2CC128 - 15224 - 48
451GLUGLUILEILE2DD128 - 15224 - 48
161ASNASNALAALA5AA153 - 15749 - 53
261ASNASNALAALA5BB153 - 15749 - 53
361ASNASNALAALA5CC153 - 15749 - 53
461ASNASNALAALA5DD153 - 15749 - 53
171ASPASPGLYGLY1AA158 - 16954 - 65
271ASPASPGLYGLY1BB158 - 16954 - 65
371ASPASPGLYGLY1CC158 - 16954 - 65
471ASPASPGLYGLY1DD158 - 16954 - 65
181ASPASPHISHIS5AA170 - 17266 - 68
281ASPASPHISHIS5BB170 - 17266 - 68
381ASPASPHISHIS5CC170 - 17266 - 68
481ASPASPHISHIS5DD170 - 17266 - 68
191ALAALAGLYGLY1AA173 - 17669 - 72
291ALAALAGLYGLY1BB173 - 17669 - 72
391ALAALAGLYGLY1CC173 - 17669 - 72
491ALAALAGLYGLY1DD173 - 17669 - 72
1101LYSLYSTHRTHR3AA177 - 20473 - 100
2101LYSLYSTHRTHR3BB177 - 20473 - 100
3101LYSLYSTHRTHR3CC177 - 20473 - 100
4101LYSLYSTHRTHR3DD177 - 20473 - 100
1111THRTHRTHRTHR5AA205101
2111THRTHRTHRTHR5BB205101
3111THRTHRTHRTHR5CC205101
4111THRTHRTHRTHR5DD205101
1121HISHISSERSER4AA206 - 207102 - 103
2121HISHISSERSER4BB206 - 207102 - 103
3121HISHISSERSER4CC206 - 207102 - 103
4121HISHISSERSER4DD206 - 207102 - 103
1131GLYGLYGLYGLY5AA208 - 209104 - 105
2131GLYGLYGLYGLY5BB208 - 209104 - 105
3131GLYGLYGLYGLY5CC208 - 209104 - 105
4131GLYGLYGLYGLY5DD208 - 209104 - 105
1141THRTHRPROPRO1AA210 - 232106 - 128
2141THRTHRPROPRO1BB210 - 232106 - 128
3141THRTHRPROPRO1CC210 - 232106 - 128
4141THRTHRPROPRO1DD210 - 232106 - 128
1151LYSLYSVALVAL2AA233 - 243129 - 139
2151LYSLYSVALVAL2BB233 - 243129 - 139
3151LYSLYSVALVAL2CC233 - 243129 - 139
4151LYSLYSVALVAL2DD233 - 243129 - 139
1161ASPASPPHEPHE5AA244 - 248140 - 144
2161ASPASPPHEPHE5BB244 - 248140 - 144
3161ASPASPPHEPHE5CC244 - 248140 - 144
4161ASPASPPHEPHE5DD244 - 248140 - 144
1171ARGARGARGARG2AA249145
2171ARGARGARGARG2BB249145
3171ARGARGARGARG2CC249145
4171ARGARGARGARG2DD249145
1181LEULEUSERSER1AA250 - 251146 - 147
2181LEULEUSERSER1BB250 - 251146 - 147
3181LEULEUSERSER1CC250 - 251146 - 147
4181LEULEUSERSER1DD250 - 251146 - 147
1191ALAALAASPASP4AA252 - 253148 - 149
2191ALAALAASPASP4BB252 - 253148 - 149
3191ALAALAASPASP4CC252 - 253148 - 149
4191ALAALAASPASP4DD252 - 253148 - 149
1201ASPASPILEILE1AA254 - 255150 - 151
2201ASPASPILEILE1BB254 - 255150 - 151
3201ASPASPILEILE1CC254 - 255150 - 151
4201ASPASPILEILE1DD254 - 255150 - 151
1211ARGARGARGARG3AA256152
2211ARGARGARGARG3BB256152
3211ARGARGARGARG3CC256152
4211ARGARGARGARG3DD256152
1221GLYGLYLEULEU2AA257 - 261153 - 157
2221GLYGLYLEULEU2BB257 - 261153 - 157
3221GLYGLYLEULEU2CC257 - 261153 - 157
4221GLYGLYLEULEU2DD257 - 261153 - 157
1231TYRTYRGLYGLY4AA262 - 263158 - 159
2231TYRTYRGLYGLY4BB262 - 263158 - 159
3231TYRTYRGLYGLY4CC262 - 263158 - 159
4231TYRTYRGLYGLY4DD262 - 263158 - 159
112CGSCGSCGSCGS4AN1273
212CGSCGSCGSCGS4BT1269
312CGSCGSCGSCGS4CDA1273
412CGSCGSCGSCGS4DNA1273

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(-0.82, 0.221, 0.528), (-0.233, -0.971, 0.044), (0.523, -0.087, 0.848)-35.4433, 23.4006, 42.3582
2given(-0.183, 0.732, 0.656), (0.742, -0.335, 0.58), (0.645, 0.593, -0.482)-22.1106, 66.2545, -47.7774
3given(-0.706, 0.293, 0.645), (-0.618, 0.189, -0.763), (-0.346, -0.937, 0.048)-9.9366, 11.2619, 14.7857

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
MACROPHAGE METALLOELASTASE / MME / MATRIX METALLOPROTEINASE-12 / MACROPHAGE ELASTASE / ME / HME / MMP-12


Mass: 18280.455 Da / Num. of mol.: 4 / Fragment: CATALYTIC DOMAIN, RESIDUES 106-263 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: COMPOUND EXPRESSED WITH A 5XHIS TAG AT THE C-TERMINUS FOR CLONING/PURIFICATION PURPOSES
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P39900, macrophage elastase

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Non-polymers , 7 types, 719 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-CGS / N-HYDROXY-2(R)-[[(4-METHOXYPHENYL)SULFONYL](3-PICOLYL)AMINO]-3-METHYLBUTANAMIDE HYDROCHLORIDE / CGS-27023A


Mass: 393.457 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H23N3O5S
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 683 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 219 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 219 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, GLU 219 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 219 TO ALA ENGINEERED RESIDUE IN CHAIN C, GLU 219 TO ALA ENGINEERED RESIDUE IN CHAIN D, GLU 219 TO ALA
Sequence detailsINACTIVATION MUTATION MADE E219A.

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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: 2.05 Å3/Da / Density % sol: 40.14 % / Description: NONE
Crystal growTemperature: 291 K / pH: 6.2
Details: 100 MM IMIDAZOLE,1.1-1.6 M SODIUM ACETATE, 1 MM 1,3-DIAMINO-PROPANE, PH 6.2, 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.9801
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 11, 2005 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2→31.1 Å / Num. obs: 38877 / % possible obs: 97.4 % / Observed criterion σ(I): 1 / Redundancy: 4 % / Biso Wilson estimate: 13.02 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.8
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 3.7 / % possible all: 87.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IN HOUSE COORDINATES

Resolution: 2→33.71 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.883 / SU B: 9.974 / SU ML: 0.128 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.242 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. MOLECULES C AND D INCLUDE A CLONING METHIONINE ARTIFACT AT THE N-TERMINUS, LABELLED RESIDUE 105. MOLECULE A HAS WEAK INDICATIONS OF THE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. MOLECULES C AND D INCLUDE A CLONING METHIONINE ARTIFACT AT THE N-TERMINUS, LABELLED RESIDUE 105. MOLECULE A HAS WEAK INDICATIONS OF THE SAME BUT NOT INCLUDE IN THE MODEL. DUE TO STERIC CONSTRAINTS THE AMIDE BOND 106-107 IN MOLECULE B IS UNUSUAL.
RfactorNum. reflection% reflectionSelection details
Rfree0.23683 1948 5 %RANDOM
Rwork0.17868 ---
obs0.18157 36902 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 5.68 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å2-0.22 Å2
2---0.17 Å20 Å2
3---0.29 Å2
Refinement stepCycle: LAST / Resolution: 2→33.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4964 0 161 683 5808
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225458
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2541.9367322
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3435670
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.10422.885253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.54815780
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8451528
X-RAY DIFFRACTIONr_chiral_restr0.090.2748
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024286
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1930.22574
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.23679
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2526
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0850.213
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2460.2182
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.220.254
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2941.53254
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.51125134
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.96932300
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.3534.52169
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

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A576tight positional0.060.05
12B576tight positional0.060.05
13C576tight positional0.050.05
14D576tight positional0.080.05
11A443medium positional0.660.5
12B443medium positional0.660.5
13C443medium positional0.520.5
14D443medium positional0.680.5
21A27medium positional0.090.5
22B27medium positional0.070.5
23C27medium positional0.080.5
24D27medium positional0.080.5
11A150loose positional1.255
12B150loose positional0.915
13C150loose positional0.775
14D150loose positional1.115
11A576tight thermal0.080.5
12B576tight thermal0.10.5
13C576tight thermal0.090.5
14D576tight thermal0.090.5
11A443medium thermal0.552
12B443medium thermal0.72
13C443medium thermal0.652
14D443medium thermal0.632
21A27medium thermal0.412
22B27medium thermal0.492
23C27medium thermal0.452
24D27medium thermal0.42
11A150loose thermal0.9310
12B150loose thermal1.9210
13C150loose thermal1.7610
14D150loose thermal1.3710
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 113 -
Rwork0.182 2184 -
obs--100 %
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)
11.5719-0.9298-0.20111.49370.24131.8502-0.0229-0.0415-0.2260.04450.01890.11190.3491-0.14820.0040.0087-0.05570.0042-0.05920.0009-0.0417-14.58815.5689-18.3802
22.1313-0.3567-0.21821.1580.10590.62230.0044-0.03760.06530.0143-0.00670.0619-0.0419-0.02610.0023-0.0735-0.0043-0.0035-0.09990.0009-0.0693-29.735610.840917.7763
32.019-0.55040.11541.62540.01071.37480.05780.12880.0085-0.1438-0.05610.0644-0.0082-0.0806-0.0017-0.0729-0.0018-0.0142-0.04950.0003-0.081-20.114139.5947-38.994
41.80630.5424-0.15121.1491-0.33720.78190.0191-0.1040.01880.0796-0.01920.0118-0.0159-0.02390.0001-0.07440.00640.0013-0.0882-0.0072-0.0743-7.01137.20694.3055
50.1178-0.0770.31390.0651-0.38913.12550.05270.0438-0.0223-0.0438-0.11680.13230.11550.19120.06410.0051-0.02250.00140.006-0.01950.0182-5.608533.5341-14.4804
67.303111.88751.47419.34962.39930.29750.80290.1980.45560.6163-0.45220.21980.2162-0.6464-0.35070.0015-0.00170.00170.0018-0.0028-0.0008-13.767125.2955-24.6196
76.1052-7.05850.19638.3653-0.80441.6360.23070.0942-0.3399-0.8689-0.0991-0.4530.07420.1064-0.13160.00040.0001-0.00040.0007-0.00010.0006-31.48640.834412.2071
80.83563.4910.244914.58461.02330.0718-0.08310.5896-0.5169-0.0780.15720.2201-0.26771.0431-0.0741-0.0023-0.00230.00260.00040.0003-0.0001-17.279233.2352-29.7293
97.828-7.176-4.52127.76243.99152.63110.67790.09610.1959-0.15090.1308-0.30290.2146-0.0215-0.8087-0.00090.00260.00180.0003-0.0010.0008-8.635743.2876-5.3643
100.06060.00080.01830.1219-0.12070.2748-0.01130.0098-0.0275-0.01280.00870.00080.0505-0.02720.00260.0432-0.0012-0.00610.0746-0.00240.0622-16.515524.3742-6.4932
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A106 - 263
2X-RAY DIFFRACTION2B106 - 263
3X-RAY DIFFRACTION3C105 - 263
4X-RAY DIFFRACTION4D105 - 263
5X-RAY DIFFRACTION5A1269 - 1272
6X-RAY DIFFRACTION5C1269 - 1272
7X-RAY DIFFRACTION5D1269 - 1272
8X-RAY DIFFRACTION6A1273
9X-RAY DIFFRACTION7B1269
10X-RAY DIFFRACTION8C1273
11X-RAY DIFFRACTION9D1273
12X-RAY DIFFRACTION10A2001 - 2197
13X-RAY DIFFRACTION10B2001 - 2170
14X-RAY DIFFRACTION10C2001 - 2145
15X-RAY DIFFRACTION10D2001 - 2171

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