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- PDB-4qae: Crystal structure of an engineered lipocalin (Anticalin) in compl... -

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Basic information

Entry
Database: PDB / ID: 4qae
TitleCrystal structure of an engineered lipocalin (Anticalin) in complex with human hepcidin
Components
  • Hepcidin
  • Neutrophil gelatinase-associated lipocalin
KeywordsTRANSPORT PROTEIN/SIGNALING PROTEIN / beta-barrel / engineered lipocalin / binding protein / protein-peptide complex / TRANSPORT PROTEIN-SIGNALING PROTEIN complex
Function / homology
Function and homology information


negative regulation of iron export across plasma membrane / negative regulation of intestinal absorption / positive regulation of iron ion import across plasma membrane / positive regulation of hippocampal neuron apoptotic process / positive regulation of endothelial tube morphogenesis / negative regulation of hippocampal neuron apoptotic process / positive regulation of cell projection organization / Metal sequestration by antimicrobial proteins / siderophore transport / response to kainic acid ...negative regulation of iron export across plasma membrane / negative regulation of intestinal absorption / positive regulation of iron ion import across plasma membrane / positive regulation of hippocampal neuron apoptotic process / positive regulation of endothelial tube morphogenesis / negative regulation of hippocampal neuron apoptotic process / positive regulation of cell projection organization / Metal sequestration by antimicrobial proteins / siderophore transport / response to kainic acid / response to mycotoxin / response to blue light / cellular response to increased oxygen levels / response to fructose / cellular response to X-ray / short-term memory / cellular response to interleukin-6 / iron ion sequestering activity / negative regulation of iron ion transmembrane transport / enterobactin binding / response to iron ion / response to herbicide / response to iron(II) ion / transporter regulator activity / positive regulation of reactive oxygen species biosynthetic process / cellular response to interleukin-1 / long-term memory / defense response to fungus / cellular response to nutrient levels / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of endothelial cell migration / Iron uptake and transport / acute-phase response / hormone activity / cellular response to nerve growth factor stimulus / response to virus / multicellular organismal-level iron ion homeostasis / specific granule lumen / cellular response to hydrogen peroxide / cellular response to amyloid-beta / cellular response to tumor necrosis factor / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of cold-induced thermogenesis / cellular response to lipopolysaccharide / protease binding / Interleukin-4 and Interleukin-13 signaling / cellular response to hypoxia / killing of cells of another organism / intracellular iron ion homeostasis / defense response to bacterium / immune response / iron ion binding / response to xenobiotic stimulus / innate immune response / Neutrophil degranulation / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Hepcidin / Hepcidin / Neutrophil gelatinase-associated lipocalin/epididymal-specific lipocalin-12 / Lipocalin / Lipocalin family conserved site / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin ...Hepcidin / Hepcidin / Neutrophil gelatinase-associated lipocalin/epididymal-specific lipocalin-12 / Lipocalin / Lipocalin family conserved site / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Neutrophil gelatinase-associated lipocalin / Hepcidin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsGiese, T. / Skerra, A.
CitationJournal: To be Published
Title: Structure of a hepcidin-binding anticalin in complex with its peptide ligand
Authors: Giese, T. / Skerra, A.
History
DepositionMay 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
P: Hepcidin
Q: Hepcidin
R: Hepcidin
S: Hepcidin
T: Hepcidin
U: Hepcidin
A: Neutrophil gelatinase-associated lipocalin
B: Neutrophil gelatinase-associated lipocalin
C: Neutrophil gelatinase-associated lipocalin
D: Neutrophil gelatinase-associated lipocalin
E: Neutrophil gelatinase-associated lipocalin
F: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,92225
Polymers145,79912
Non-polymers1,12313
Water11,331629
1
P: Hepcidin
A: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4534
Polymers24,3002
Non-polymers1542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-32 kcal/mol
Surface area10490 Å2
MethodPISA
2
Q: Hepcidin
B: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4534
Polymers24,3002
Non-polymers1542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-34 kcal/mol
Surface area10290 Å2
MethodPISA
3
R: Hepcidin
C: Neutrophil gelatinase-associated lipocalin


Theoretical massNumber of molelcules
Total (without water)24,3002
Polymers24,3002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-27 kcal/mol
Surface area9960 Å2
MethodPISA
4
S: Hepcidin
D: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4895
Polymers24,3002
Non-polymers1893
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-39 kcal/mol
Surface area9880 Å2
MethodPISA
5
T: Hepcidin
E: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5364
Polymers24,3002
Non-polymers2362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-24 kcal/mol
Surface area9790 Å2
MethodPISA
6
U: Hepcidin
F: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6906
Polymers24,3002
Non-polymers3904
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-33 kcal/mol
Surface area10020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.894, 126.894, 156.707
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein/peptide
Hepcidin / Liver-expressed antimicrobial peptide 1 / LEAP-1 / Putative liver tumor regressor / PLTR / Hepcidin- ...Liver-expressed antimicrobial peptide 1 / LEAP-1 / Putative liver tumor regressor / PLTR / Hepcidin-25 / Hepc25 / Hepcidin-20 / Hepc20


Mass: 2802.455 Da / Num. of mol.: 6 / Fragment: UNP residues 60-84 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P81172
#2: Protein
Neutrophil gelatinase-associated lipocalin / NGAL / 25 kDa alpha-2-microglobulin-related subunit of MMP-9 / Lipocalin-2 / Oncogene 24p3 / ...NGAL / 25 kDa alpha-2-microglobulin-related subunit of MMP-9 / Lipocalin-2 / Oncogene 24p3 / Siderocalin LCN2 / p25


Mass: 21497.367 Da / Num. of mol.: 6 / Fragment: UNP residues 21-198
Mutation: Q28H,A40E,I41V,Q49M,Y52W,K59E,S68I,L70M,F71P,R72L,K73A,K74E,D77E,W79L,I80F,R81Q,C87S,N96G,Y100G,L103R,Y106G,K125V,S127W,Y132V,K134W,I135V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: engineered variant, HNL, LCN2, NGAL / Plasmid: pEX2200-I24 / Production host: Escherichia coli (E. coli) / Strain (production host): JM83 / References: UniProt: P80188
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 629 / Source method: isolated from a natural source / Formula: H2O
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: 2.5 Å3/Da / Density % sol: 50.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 0.1 M HEPES/NaOH, 47% w/v MPD, pH 6.6, VAPOR DIFFUSION, HANGING DROPS, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 2 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 18, 2010 / Details: mirrors
RadiationMonochromator: sagittally bent Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2 Å / Relative weight: 1
ReflectionResolution: 2.1→35 Å / Num. all: 162481 / Num. obs: 162157 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.33 % / Biso Wilson estimate: 37.056 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 19.1
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.1-2.160.6682.836050311862198.8
2.16-2.220.5584.459812511713199.7
2.22-2.290.4436.1911530911369199.8
2.29-2.360.397.0711482311040199.9
2.36-2.440.3288.47114483107691100
2.44-2.520.25110.67112094103661100
2.52-2.620.20812.3410866999651100
2.62-2.720.17614.1610568996351100
2.72-2.850.13617.3310193092351100
2.85-2.980.10321.399772588101100
2.98-3.150.08524.779354984041100
3.15-3.340.07328.328873379501100
3.34-3.570.06132.868303574251100
3.57-3.850.05635.69783096967199.9
3.85-4.220.0538.917147563801100
4.22-4.720.04442.546478657651100
4.72-5.450.04341.855787050931100
5.45-6.670.04442.054962743121100
6.67-9.440.03945.333820032951100
9.44-350.03449.81208871802197.9

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
XDSdata reduction
Auto-Rickshawphasing
RefinementResolution: 2.1→33.18 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.2035 / WRfactor Rwork: 0.1643 / FOM work R set: 0.8245 / SU B: 7.376 / SU ML: 0.105 / SU R Cruickshank DPI: 0.1744 / SU Rfree: 0.1547 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2065 4267 5 %RANDOM
Rwork0.1661 80956 --
obs0.1681 80956 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 144.28 Å2 / Biso mean: 39.088 Å2 / Biso min: 12.75 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0.05 Å2-0 Å2
2---0.1 Å20 Å2
3---0.32 Å2
Refinement stepCycle: LAST / Resolution: 2.1→33.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9240 0 69 629 9938
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0199576
X-RAY DIFFRACTIONr_bond_other_d0.0010.029003
X-RAY DIFFRACTIONr_angle_refined_deg1.5951.95513003
X-RAY DIFFRACTIONr_angle_other_deg0.812320775
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.72451133
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.82324.404436
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.761151608
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.991538
X-RAY DIFFRACTIONr_chiral_restr0.0940.21406
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02110609
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022225
X-RAY DIFFRACTIONr_mcbond_it1.0741.4094580
X-RAY DIFFRACTIONr_mcbond_other1.071.4094579
X-RAY DIFFRACTIONr_mcangle_it1.8062.0975697
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 341 -
Rwork0.223 5796 -
all-6137 -
obs--98.29 %
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)
14.58722.1235-0.66781.81311.42774.29110.0876-0.542-0.74860.3850.1081-0.40190.97990.851-0.19570.31610.1324-0.08140.25290.0280.2468122.387915.2343-22.6498
28.3691-5.50352.57459.5968-4.32436.94680.1692-0.0356-0.5864-0.22930.17350.47880.6111-0.0933-0.34270.1033-0.00710.00960.1236-0.02590.0805115.518119.975-26.0208
315.3017-3.92370.3981.0385-0.06230.27750.31640.23150.3618-0.1491-0.1374-0.1449-0.1830.1509-0.17910.32910.02590.0330.45830.02020.329130.433521.68370.1117
49.83260.84330.24916.6658-0.25456.806-0.1109-0.53420.29440.3414-0.0291-0.3413-0.01050.43170.140.0940.0255-0.03880.099-0.00690.0557113.370621.6022-2.3863
56.9805-8.7765-5.078414.37369.1577.6889-0.3781-0.3113-0.333-0.00250.42310.20190.40360.4068-0.0450.3007-0.00240.00040.29070.00980.3399137.352328.1531-19.165
67.6584-2.72-2.3969.31272.04946.76050.15540.12940.2607-0.3906-0.0287-0.4092-0.29830.514-0.12670.0919-0.0891-0.01160.2041-0.08010.2131125.772239.5441-13.8985
726.0694-5.091-13.98541.05552.74287.53190.2087-0.1263-0.1087-0.0409-0.15460.0558-0.11970.0214-0.05410.3246-0.0138-0.00650.5232-0.0440.537482.887959.8668-14.0962
810.4055-0.2899-2.24315.55780.55056.56130.1386-0.42450.40750.2739-0.0048-0.0483-0.5261-0.0584-0.13380.28670.04820.06560.04020.03820.191698.354455.3787-19.5811
96.37890.49022.72537.3748-3.49675.11630.11210.3590.6966-0.2311-0.26740.3231-0.5674-0.26770.15530.31650.1626-0.00570.25660.03490.126187.100637.953-31.4382
103.529-0.3371-0.570810.22622.61610.8147-0.12160.32810.6194-0.98650.2011-0.093-0.3355-0.114-0.07950.26730.0903-0.04110.28380.03540.218186.705639.784-32.7906
1111.4105-2.51467.87831.1708-0.8036.8886-0.07590.42520.1251-0.1627-0.27890.1797-0.26840.0630.35480.33510.0165-0.03020.39580.03170.379270.895240.9914-18.1425
128.2295-0.71231.02366.3085-1.07086.89430.19110.0206-0.2750.0569-0.05870.48170.0866-0.6761-0.13240.11420.02320.06250.1696-0.03850.114585.333838.2022-6.8862
138.66293.5908-0.37243.34540.44590.4154-0.07430.3906-0.2696-0.11480.1163-0.01010.0599-0.0253-0.0420.22020.03630.01390.25880.00150.147120.963920.3586-46.1901
140.9065-0.2952-0.86461.79230.48323.03530.1375-0.09470.1959-0.03550.106-0.2088-0.08220.4683-0.24340.0607-0.00640.05220.134-0.03280.1194126.577429.4723-31.6531
153.7171.67970.406510.65664.56982.0038-0.06470.4177-0.854-0.30170.2367-0.6194-0.03890.1134-0.17190.7241-0.01710.02420.649-0.04690.6854128.62169.1598-33.5276
163.14060.5919-0.86183.17590.29713.26840.1250.31880.2641-0.31590.0344-0.0079-0.1627-0.0461-0.15940.07970.02030.0550.13730.0170.0646120.629130.3929-39.0573
170.4555-2.0082-0.345613.96391.95980.36790.0486-0.1060.26850.06560.0452-0.168-0.1288-0.0618-0.09380.30560.0211-0.01430.3989-0.09980.407499.998820.61078.3725
181.4744-0.54710.51023.6242-1.02653.675-0.0771-0.1049-0.14430.05040.02850.00060.4530.13350.04860.09510.0192-0.00460.0220.02840.0477106.36278.5802-7.4795
191.8811-0.34150.79448.5017-4.53733.8008-0.0333-0.4712-0.1520.743-0.0828-0.45390.00430.44270.11610.23130.1774-0.02320.38260.00710.0999117.56399.2396-7.2252
202.47290.064-0.65014.07090.45475.0147-0.095-0.1528-0.17710.17620.07870.14570.4493-0.08950.01630.12750.01380.02720.02460.03380.058103.29679.8903-5.7711
211.8075-1.45492.07315.2059-5.496711.9363-0.242-0.24490.50230.2866-0.0676-0.4772-0.6987-0.01150.30950.388-0.165-0.06780.4293-0.13280.556133.166652.8162-0.8287
224.36650.94650.49831.4091.11513.53150.0849-0.45260.21070.23540.0001-0.3252-0.12730.186-0.0850.133-0.0757-0.04730.2082-0.13880.2084121.613740.34620.2512
233.59611.96541.44683.04441.22942.5189-0.052-0.05660.12370.20720.1145-0.7658-0.20090.8089-0.06240.1614-0.0884-0.1370.4413-0.08340.401129.713237.38331.1114
243.47950.2567-0.54464.20180.34674.49430.0984-0.39870.59090.39460.0288-0.2775-0.7090.3396-0.12720.2425-0.0891-0.08220.2251-0.15540.2765121.39347.3421-1.1731
252.0977-0.61190.18342.9055-0.59883.77970.07390.15520.4851-0.2067-0.0717-0.0547-0.5455-0.0927-0.00220.34620.0680.12010.06640.10180.2469100.415856.6579-34.038
261.85770.1102-0.29614.3497-2.081.94360.05710.16470.67990.1320.06040.0949-0.6069-0.2727-0.11750.450.12040.04490.13010.10950.312296.002858.4287-34.4065
273.93941.01530.65231.3898-0.02775.39080.15520.15180.6034-0.0124-0.1303-0.1901-0.53820.0007-0.02490.39320.03430.10850.05450.12020.2883103.107857.9852-30.7213
282.82440.5952-2.33073.747-1.56646.26020.07910.36520.2104-0.55650.012-0.6914-0.5060.5619-0.09120.3536-0.05040.18050.26380.06880.2838110.906652.7855-34.23
298.95013.7629-4.10735.2485-1.50017.7866-0.08470.7007-0.3885-0.5090.0567-0.20710.1137-0.24290.02790.22080.0053-0.12040.2449-0.06010.222182.300619.8222-39.3891
301.65170.57530.47582.44480.38893.29010.1210.04910.1214-0.1436-0.21280.4871-0.1213-0.83320.09180.04660.0358-0.04860.2747-0.01670.164179.759528.1566-23.1027
311.4732-0.26863.29452.5011-0.51697.46820.00330.0108-0.0028-0.43170.13260.1474-0.16280.0606-0.13590.43850.00220.0330.43480.02260.458577.270935.9242-34.8768
323.12460.402-0.2233.62110.38194.54710.07910.1479-0.2726-0.1414-0.10730.26170.3709-0.46040.02820.0627-0.0478-0.05340.1547-0.04590.135983.986920.2503-27.1376
333.4899-1.2711-0.5217.42274.11613.47350.0065-0.005-0.06830.0659-0.06390.16490.0725-0.21640.05740.27020.00510.01970.26480.03660.201484.361137.714211.9324
343.30670.1453-0.73474.18951.54823.57630.0299-0.3470.4350.28220.1147-0.0192-0.339-0.1257-0.14460.19620.04260.03180.1656-0.06750.101190.921551.87914.9842
352.8046-0.1852-1.79881.19561.4743.05090.29030.07120.2499-0.113-0.15380.0995-0.4482-0.4936-0.13650.21640.13090.09850.26870.01540.193388.170950.8706-4.3051
363.08620.317-0.46224.73840.45313.50450.0935-0.43470.12530.5191-0.0177-0.0774-0.0388-0.0835-0.07580.22360.05130.04050.1816-0.07560.081793.095646.38885.4641
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1P1 - 15
2X-RAY DIFFRACTION2P16 - 25
3X-RAY DIFFRACTION3Q2 - 6
4X-RAY DIFFRACTION4Q7 - 25
5X-RAY DIFFRACTION5R2 - 6
6X-RAY DIFFRACTION6R7 - 25
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