HEADER IMMUNE SYSTEM 02-MAR-11 3QXW TITLE FREE STRUCTURE OF AN ANTI-METHOTREXATE CDR1-4 GRAFT VHH ANTIBODY COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTI-METHOTREXATE CDR1-4 GRAFT VHH; COMPND 3 CHAIN: A, B, C, D, E; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LAMA GLAMA; SOURCE 3 ORGANISM_COMMON: LLAMA; SOURCE 4 ORGANISM_TAXID: 9844; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET21(A)+ KEYWDS CAMELID SINGLE DOMAIN ANTIBODY, HEAVY CHAIN ONLY, VHH, ANTIBODY, KEYWDS 2 ANTI-HAPTEN ANTIBODY, CDR, HAPTEN BINDING, SMALL MOLECULE SENSING, KEYWDS 3 LIGAND BINDING, LOW MOLECULAR WEIGHT COMPOUND, METHOTREXATE, IMMUNE KEYWDS 4 SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR S.W.FANNING,J.R.HORN REVDAT 3 25-DEC-19 3QXW 1 REMARK REVDAT 2 11-SEP-13 3QXW 1 SOURCE REVDAT 1 27-JUL-11 3QXW 0 JRNL AUTH S.W.FANNING,J.R.HORN JRNL TITL AN ANTI-HAPTEN CAMELID ANTIBODY REVEALS A CRYPTIC BINDING JRNL TITL 2 SITE WITH SIGNIFICANT ENERGETIC CONTRIBUTIONS FROM A JRNL TITL 3 NONHYPERVARIABLE LOOP. JRNL REF PROTEIN SCI. V. 20 1196 2011 JRNL REFN ISSN 0961-8368 JRNL PMID 21557375 JRNL DOI 10.1002/PRO.648 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 47518 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2525 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3402 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.34 REMARK 3 BIN R VALUE (WORKING SET) : 0.2560 REMARK 3 BIN FREE R VALUE SET COUNT : 156 REMARK 3 BIN FREE R VALUE : 0.3010 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4733 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 11 REMARK 3 SOLVENT ATOMS : 295 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.87 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.89000 REMARK 3 B22 (A**2) : 0.81000 REMARK 3 B33 (A**2) : -1.68000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.24000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.155 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.148 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.104 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.578 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.925 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4887 ; 0.018 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6622 ; 1.540 ; 1.934 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 615 ; 7.055 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 226 ;36.223 ;22.655 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 764 ;16.058 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 48 ;19.439 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 690 ; 0.153 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3777 ; 0.013 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 3045 ; 1.350 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4830 ; 2.206 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1842 ; 3.308 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1792 ; 4.828 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : E A B C D REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 E 1 E 129 4 REMARK 3 1 A 1 A 129 4 REMARK 3 1 B 1 B 129 4 REMARK 3 1 C 1 C 129 4 REMARK 3 1 D 1 D 129 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 E (A): 902 ; 0.550 ; 0.500 REMARK 3 MEDIUM POSITIONAL 1 A (A): 902 ; 0.690 ; 0.500 REMARK 3 MEDIUM POSITIONAL 1 B (A): 902 ; 0.780 ; 0.500 REMARK 3 MEDIUM POSITIONAL 1 C (A): 902 ; 0.550 ; 0.500 REMARK 3 MEDIUM POSITIONAL 1 D (A): 902 ; 0.980 ; 0.500 REMARK 3 MEDIUM THERMAL 1 E (A**2): 902 ; 2.440 ; 2.000 REMARK 3 MEDIUM THERMAL 1 A (A**2): 902 ; 1.770 ; 2.000 REMARK 3 MEDIUM THERMAL 1 B (A**2): 902 ; 1.670 ; 2.000 REMARK 3 MEDIUM THERMAL 1 C (A**2): 902 ; 2.290 ; 2.000 REMARK 3 MEDIUM THERMAL 1 D (A**2): 902 ; 1.860 ; 2.000 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 3 B 131 REMARK 3 ORIGIN FOR THE GROUP (A): 3.3180 -6.9540 48.0070 REMARK 3 T TENSOR REMARK 3 T11: 0.0299 T22: 0.0834 REMARK 3 T33: 0.0531 T12: 0.0386 REMARK 3 T13: 0.0276 T23: 0.0269 REMARK 3 L TENSOR REMARK 3 L11: 1.5976 L22: 2.3775 REMARK 3 L33: 2.3697 L12: 0.0694 REMARK 3 L13: 0.4773 L23: -0.7022 REMARK 3 S TENSOR REMARK 3 S11: -0.0281 S12: -0.0178 S13: 0.0797 REMARK 3 S21: 0.2065 S22: 0.1390 S23: 0.1981 REMARK 3 S31: -0.1641 S32: -0.1702 S33: -0.1109 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 3 A 131 REMARK 3 ORIGIN FOR THE GROUP (A): -11.5320 -33.5420 4.7150 REMARK 3 T TENSOR REMARK 3 T11: 0.0152 T22: 0.0105 REMARK 3 T33: 0.0323 T12: 0.0064 REMARK 3 T13: -0.0081 T23: -0.0012 REMARK 3 L TENSOR REMARK 3 L11: 1.5524 L22: 1.9776 REMARK 3 L33: 2.2465 L12: 0.1481 REMARK 3 L13: -0.0295 L23: 0.1467 REMARK 3 S TENSOR REMARK 3 S11: -0.0293 S12: 0.0024 S13: 0.0396 REMARK 3 S21: -0.0439 S22: -0.0007 S23: 0.1039 REMARK 3 S31: 0.1155 S32: -0.0290 S33: 0.0300 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 4 C 131 REMARK 3 ORIGIN FOR THE GROUP (A): -7.2290 -45.6610 30.6460 REMARK 3 T TENSOR REMARK 3 T11: 0.1113 T22: 0.2033 REMARK 3 T33: 0.0675 T12: 0.0598 REMARK 3 T13: 0.0020 T23: 0.0528 REMARK 3 L TENSOR REMARK 3 L11: 0.9927 L22: 3.6971 REMARK 3 L33: 1.2787 L12: -0.4336 REMARK 3 L13: 0.6110 L23: -1.1932 REMARK 3 S TENSOR REMARK 3 S11: 0.0519 S12: -0.0515 S13: -0.0238 REMARK 3 S21: 0.1825 S22: -0.1622 S23: -0.0954 REMARK 3 S31: -0.1987 S32: 0.0768 S33: 0.1103 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 4 D 131 REMARK 3 ORIGIN FOR THE GROUP (A): 13.0100 -15.4780 22.1150 REMARK 3 T TENSOR REMARK 3 T11: 0.0302 T22: 0.0601 REMARK 3 T33: 0.0347 T12: 0.0311 REMARK 3 T13: 0.0006 T23: 0.0096 REMARK 3 L TENSOR REMARK 3 L11: 1.0416 L22: 1.6399 REMARK 3 L33: 2.0623 L12: -0.3513 REMARK 3 L13: -0.1779 L23: 0.2648 REMARK 3 S TENSOR REMARK 3 S11: -0.0780 S12: 0.0030 S13: -0.0331 REMARK 3 S21: -0.0329 S22: 0.0015 S23: 0.0504 REMARK 3 S31: 0.1161 S32: 0.0534 S33: 0.0764 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : E 3 E 131 REMARK 3 ORIGIN FOR THE GROUP (A): -19.2340 -39.1620 56.6290 REMARK 3 T TENSOR REMARK 3 T11: 0.2538 T22: 0.0325 REMARK 3 T33: 0.0133 T12: -0.0122 REMARK 3 T13: -0.0226 T23: -0.0054 REMARK 3 L TENSOR REMARK 3 L11: 1.0257 L22: 1.4633 REMARK 3 L33: 2.0198 L12: -0.2043 REMARK 3 L13: 0.4238 L23: -0.1771 REMARK 3 S TENSOR REMARK 3 S11: 0.0849 S12: 0.1193 S13: -0.0355 REMARK 3 S21: -0.2362 S22: -0.0815 S23: 0.0928 REMARK 3 S31: -0.0501 S32: 0.0836 S33: -0.0034 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3QXW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-MAR-11. REMARK 100 THE DEPOSITION ID IS D_1000064241. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JUL-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR 225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50632 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.08900 REMARK 200 R SYM (I) : 0.14300 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M LITHIUM SULFATE MONOHYDRATE, 0.1M REMARK 280 BIS-TRIS, 25% PEG 3000, PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 29.58350 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4, 5 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 5 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: E REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 1 REMARK 465 SER A 2 REMARK 465 GLY B 1 REMARK 465 SER B 2 REMARK 465 GLY C 1 REMARK 465 SER C 2 REMARK 465 GLN C 3 REMARK 465 ARG C 28 REMARK 465 ARG C 29 REMARK 465 SER C 30 REMARK 465 SER C 31 REMARK 465 GLY D 1 REMARK 465 SER D 2 REMARK 465 GLN D 3 REMARK 465 GLY E 1 REMARK 465 SER E 2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ALA A 94 171.52 179.02 REMARK 500 ALA E 94 163.18 171.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH D1036 DISTANCE = 6.93 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA D2000 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH D1056 O REMARK 620 2 THR D 106 OG1 106.2 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA D 2000 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 D 3000 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 E 3000 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1I3U RELATED DB: PDB REMARK 900 THREE-DIMENSIONAL STRUCTURE OF A LLAMA VHH DOMAIN COMPLEXED WITH REMARK 900 THE DYE RR1 REMARK 900 RELATED ID: 2X6M RELATED DB: PDB REMARK 900 STRUCTURE OF A SINGLE DOMAIN CAMELID ANTIBODY FRAGMENT IN COMPLEX REMARK 900 WITH A C-TERMINAL PEPTIDE OF ALPHA-SYNUCLEIN REMARK 900 RELATED ID: 3QXT RELATED DB: PDB REMARK 900 RELATED ID: 3QXV RELATED DB: PDB REMARK 900 RELATED ID: 3QXU RELATED DB: PDB DBREF 3QXW A 1 131 PDB 3QXW 3QXW 1 131 DBREF 3QXW B 1 131 PDB 3QXW 3QXW 1 131 DBREF 3QXW C 1 131 PDB 3QXW 3QXW 1 131 DBREF 3QXW D 1 131 PDB 3QXW 3QXW 1 131 DBREF 3QXW E 1 131 PDB 3QXW 3QXW 1 131 SEQRES 1 A 126 GLY SER GLN VAL GLN LEU VAL GLU SER GLY GLY GLY LEU SEQRES 2 A 126 VAL GLN ALA GLY GLY SER LEU ARG LEU SER CYS ALA ALA SEQRES 3 A 126 SER ARG ARG SER SER ARG SER TRP ALA MET ALA TRP PHE SEQRES 4 A 126 ARG GLN ALA PRO GLY LYS GLU ARG GLU PHE VAL ALA LYS SEQRES 5 A 126 ILE SER GLY ASP GLY ARG LEU THR THR TYR GLY ASP SER SEQRES 6 A 126 VAL LYS GLY ARG PHE THR ILE SER ARG ASP ASN ALA GLU SEQRES 7 A 126 TYR LEU VAL TYR LEU GLN MET ASP SER LEU LYS PRO GLU SEQRES 8 A 126 ASP THR ALA VAL TYR TYR CYS ALA ALA ASP ASP ASN TYR SEQRES 9 A 126 VAL THR ALA SER TRP ARG SER GLY PRO ASP TYR TRP GLY SEQRES 10 A 126 GLN GLY THR GLN VAL THR VAL SER SER SEQRES 1 B 126 GLY SER GLN VAL GLN LEU VAL GLU SER GLY GLY GLY LEU SEQRES 2 B 126 VAL GLN ALA GLY GLY SER LEU ARG LEU SER CYS ALA ALA SEQRES 3 B 126 SER ARG ARG SER SER ARG SER TRP ALA MET ALA TRP PHE SEQRES 4 B 126 ARG GLN ALA PRO GLY LYS GLU ARG GLU PHE VAL ALA LYS SEQRES 5 B 126 ILE SER GLY ASP GLY ARG LEU THR THR TYR GLY ASP SER SEQRES 6 B 126 VAL LYS GLY ARG PHE THR ILE SER ARG ASP ASN ALA GLU SEQRES 7 B 126 TYR LEU VAL TYR LEU GLN MET ASP SER LEU LYS PRO GLU SEQRES 8 B 126 ASP THR ALA VAL TYR TYR CYS ALA ALA ASP ASP ASN TYR SEQRES 9 B 126 VAL THR ALA SER TRP ARG SER GLY PRO ASP TYR TRP GLY SEQRES 10 B 126 GLN GLY THR GLN VAL THR VAL SER SER SEQRES 1 C 126 GLY SER GLN VAL GLN LEU VAL GLU SER GLY GLY GLY LEU SEQRES 2 C 126 VAL GLN ALA GLY GLY SER LEU ARG LEU SER CYS ALA ALA SEQRES 3 C 126 SER ARG ARG SER SER ARG SER TRP ALA MET ALA TRP PHE SEQRES 4 C 126 ARG GLN ALA PRO GLY LYS GLU ARG GLU PHE VAL ALA LYS SEQRES 5 C 126 ILE SER GLY ASP GLY ARG LEU THR THR TYR GLY ASP SER SEQRES 6 C 126 VAL LYS GLY ARG PHE THR ILE SER ARG ASP ASN ALA GLU SEQRES 7 C 126 TYR LEU VAL TYR LEU GLN MET ASP SER LEU LYS PRO GLU SEQRES 8 C 126 ASP THR ALA VAL TYR TYR CYS ALA ALA ASP ASP ASN TYR SEQRES 9 C 126 VAL THR ALA SER TRP ARG SER GLY PRO ASP TYR TRP GLY SEQRES 10 C 126 GLN GLY THR GLN VAL THR VAL SER SER SEQRES 1 D 126 GLY SER GLN VAL GLN LEU VAL GLU SER GLY GLY GLY LEU SEQRES 2 D 126 VAL GLN ALA GLY GLY SER LEU ARG LEU SER CYS ALA ALA SEQRES 3 D 126 SER ARG ARG SER SER ARG SER TRP ALA MET ALA TRP PHE SEQRES 4 D 126 ARG GLN ALA PRO GLY LYS GLU ARG GLU PHE VAL ALA LYS SEQRES 5 D 126 ILE SER GLY ASP GLY ARG LEU THR THR TYR GLY ASP SER SEQRES 6 D 126 VAL LYS GLY ARG PHE THR ILE SER ARG ASP ASN ALA GLU SEQRES 7 D 126 TYR LEU VAL TYR LEU GLN MET ASP SER LEU LYS PRO GLU SEQRES 8 D 126 ASP THR ALA VAL TYR TYR CYS ALA ALA ASP ASP ASN TYR SEQRES 9 D 126 VAL THR ALA SER TRP ARG SER GLY PRO ASP TYR TRP GLY SEQRES 10 D 126 GLN GLY THR GLN VAL THR VAL SER SER SEQRES 1 E 126 GLY SER GLN VAL GLN LEU VAL GLU SER GLY GLY GLY LEU SEQRES 2 E 126 VAL GLN ALA GLY GLY SER LEU ARG LEU SER CYS ALA ALA SEQRES 3 E 126 SER ARG ARG SER SER ARG SER TRP ALA MET ALA TRP PHE SEQRES 4 E 126 ARG GLN ALA PRO GLY LYS GLU ARG GLU PHE VAL ALA LYS SEQRES 5 E 126 ILE SER GLY ASP GLY ARG LEU THR THR TYR GLY ASP SER SEQRES 6 E 126 VAL LYS GLY ARG PHE THR ILE SER ARG ASP ASN ALA GLU SEQRES 7 E 126 TYR LEU VAL TYR LEU GLN MET ASP SER LEU LYS PRO GLU SEQRES 8 E 126 ASP THR ALA VAL TYR TYR CYS ALA ALA ASP ASP ASN TYR SEQRES 9 E 126 VAL THR ALA SER TRP ARG SER GLY PRO ASP TYR TRP GLY SEQRES 10 E 126 GLN GLY THR GLN VAL THR VAL SER SER HET NA D2000 1 HET SO4 D3000 5 HET SO4 E3000 5 HETNAM NA SODIUM ION HETNAM SO4 SULFATE ION FORMUL 6 NA NA 1+ FORMUL 7 SO4 2(O4 S 2-) FORMUL 9 HOH *295(H2 O) HELIX 1 1 ARG A 28 TRP A 34 5 7 HELIX 2 2 ASP A 64 LYS A 67 5 4 HELIX 3 3 LYS A 89 THR A 93 5 5 HELIX 4 4 TYR A 104 TRP A 109 5 6 HELIX 5 5 ARG B 28 TRP B 34 5 7 HELIX 6 6 LYS B 89 THR B 93 5 5 HELIX 7 7 TYR B 104 TRP B 109 5 6 HELIX 8 11 LYS C 89 THR C 93 5 5 HELIX 9 12 VAL C 105 TRP C 109 5 5 HELIX 10 8 ASP D 64 LYS D 67 5 4 HELIX 11 9 LYS D 89 THR D 93 5 5 HELIX 12 10 TYR D 104 TRP D 109 5 6 HELIX 13 13 ASP E 64 LYS E 67 5 4 HELIX 14 14 LYS E 89 THR E 93 5 5 HELIX 15 15 TYR E 104 TRP E 109 5 6 SHEET 1 A 4 LEU A 6 SER A 9 0 SHEET 2 A 4 LEU A 20 ALA A 26 -1 O ALA A 25 N VAL A 7 SHEET 3 A 4 LEU A 80 MET A 85 -1 O MET A 85 N LEU A 20 SHEET 4 A 4 PHE A 70 ASP A 75 -1 N ASP A 75 O LEU A 80 SHEET 1 B 6 GLY A 12 GLN A 15 0 SHEET 2 B 6 THR A 125 SER A 130 1 O THR A 128 N GLY A 12 SHEET 3 B 6 ALA A 94 ASP A 101 -1 N TYR A 96 O THR A 125 SHEET 4 B 6 ALA A 35 GLN A 41 -1 N ALA A 37 O ALA A 99 SHEET 5 B 6 GLU A 48 ILE A 53 -1 O GLU A 48 N ARG A 40 SHEET 6 B 6 THR A 60 TYR A 62 -1 O THR A 61 N LYS A 52 SHEET 1 C 4 GLY A 12 GLN A 15 0 SHEET 2 C 4 THR A 125 SER A 130 1 O THR A 128 N GLY A 12 SHEET 3 C 4 ALA A 94 ASP A 101 -1 N TYR A 96 O THR A 125 SHEET 4 C 4 TYR A 120 TRP A 121 -1 O TYR A 120 N ALA A 100 SHEET 1 D 4 LEU B 6 SER B 9 0 SHEET 2 D 4 LEU B 20 ALA B 26 -1 O SER B 23 N SER B 9 SHEET 3 D 4 LEU B 80 MET B 85 -1 O MET B 85 N LEU B 20 SHEET 4 D 4 PHE B 70 ASP B 75 -1 N SER B 73 O TYR B 82 SHEET 1 E 6 GLY B 12 GLN B 15 0 SHEET 2 E 6 THR B 125 SER B 130 1 O THR B 128 N VAL B 14 SHEET 3 E 6 ALA B 94 ASP B 101 -1 N TYR B 96 O THR B 125 SHEET 4 E 6 ALA B 35 GLN B 41 -1 N PHE B 39 O TYR B 97 SHEET 5 E 6 GLU B 48 ILE B 53 -1 O GLU B 48 N ARG B 40 SHEET 6 E 6 THR B 60 TYR B 62 -1 O THR B 61 N LYS B 52 SHEET 1 F 4 GLY B 12 GLN B 15 0 SHEET 2 F 4 THR B 125 SER B 130 1 O THR B 128 N VAL B 14 SHEET 3 F 4 ALA B 94 ASP B 101 -1 N TYR B 96 O THR B 125 SHEET 4 F 4 TYR B 120 TRP B 121 -1 O TYR B 120 N ALA B 100 SHEET 1 G 4 LEU D 6 SER D 9 0 SHEET 2 G 4 LEU D 20 ALA D 26 -1 O ALA D 25 N VAL D 7 SHEET 3 G 4 LEU D 80 MET D 85 -1 O MET D 85 N LEU D 20 SHEET 4 G 4 PHE D 70 ASP D 75 -1 N THR D 71 O GLN D 84 SHEET 1 H 6 GLY D 12 GLN D 15 0 SHEET 2 H 6 THR D 125 SER D 130 1 O THR D 128 N GLY D 12 SHEET 3 H 6 ALA D 94 ASP D 101 -1 N ALA D 94 O VAL D 127 SHEET 4 H 6 ALA D 35 GLN D 41 -1 N GLN D 41 O VAL D 95 SHEET 5 H 6 GLU D 48 ILE D 53 -1 O ALA D 51 N TRP D 38 SHEET 6 H 6 THR D 60 TYR D 62 -1 O THR D 61 N LYS D 52 SHEET 1 I 4 GLY D 12 GLN D 15 0 SHEET 2 I 4 THR D 125 SER D 130 1 O THR D 128 N GLY D 12 SHEET 3 I 4 ALA D 94 ASP D 101 -1 N ALA D 94 O VAL D 127 SHEET 4 I 4 TYR D 120 TRP D 121 -1 O TYR D 120 N ALA D 100 SHEET 1 J 4 LEU C 6 SER C 9 0 SHEET 2 J 4 LEU C 20 ALA C 26 -1 O SER C 23 N SER C 9 SHEET 3 J 4 LEU C 80 MET C 85 -1 O MET C 85 N LEU C 20 SHEET 4 J 4 PHE C 70 ASP C 75 -1 N THR C 71 O GLN C 84 SHEET 1 K 6 LEU C 13 GLN C 15 0 SHEET 2 K 6 THR C 125 SER C 130 1 O SER C 130 N VAL C 14 SHEET 3 K 6 ALA C 94 ASP C 101 -1 N TYR C 96 O THR C 125 SHEET 4 K 6 ALA C 35 GLN C 41 -1 N ALA C 37 O ALA C 99 SHEET 5 K 6 GLU C 48 ILE C 53 -1 O GLU C 48 N ARG C 40 SHEET 6 K 6 THR C 60 TYR C 62 -1 O THR C 61 N LYS C 52 SHEET 1 L 4 LEU C 13 GLN C 15 0 SHEET 2 L 4 THR C 125 SER C 130 1 O SER C 130 N VAL C 14 SHEET 3 L 4 ALA C 94 ASP C 101 -1 N TYR C 96 O THR C 125 SHEET 4 L 4 TYR C 120 TRP C 121 -1 O TYR C 120 N ALA C 100 SHEET 1 M 4 GLN E 5 SER E 9 0 SHEET 2 M 4 LEU E 20 SER E 27 -1 O SER E 27 N GLN E 5 SHEET 3 M 4 LEU E 80 MET E 85 -1 O LEU E 83 N LEU E 22 SHEET 4 M 4 PHE E 70 ASP E 75 -1 N THR E 71 O GLN E 84 SHEET 1 N 6 GLY E 12 GLN E 15 0 SHEET 2 N 6 THR E 125 SER E 130 1 O SER E 130 N VAL E 14 SHEET 3 N 6 ALA E 94 ASP E 101 -1 N TYR E 96 O THR E 125 SHEET 4 N 6 ALA E 35 GLN E 41 -1 N PHE E 39 O TYR E 97 SHEET 5 N 6 GLU E 48 ILE E 53 -1 O GLU E 48 N ARG E 40 SHEET 6 N 6 THR E 60 TYR E 62 -1 O THR E 61 N LYS E 52 SHEET 1 O 4 GLY E 12 GLN E 15 0 SHEET 2 O 4 THR E 125 SER E 130 1 O SER E 130 N VAL E 14 SHEET 3 O 4 ALA E 94 ASP E 101 -1 N TYR E 96 O THR E 125 SHEET 4 O 4 TYR E 120 TRP E 121 -1 O TYR E 120 N ALA E 100 SSBOND 1 CYS A 24 CYS A 98 1555 1555 2.07 SSBOND 2 CYS B 24 CYS B 98 1555 1555 2.09 SSBOND 3 CYS C 24 CYS C 98 1555 1555 2.09 SSBOND 4 CYS D 24 CYS D 98 1555 1555 2.15 SSBOND 5 CYS E 24 CYS E 98 1555 1555 2.05 LINK NA NA D2000 O HOH D1056 1555 1555 2.30 LINK OG1 THR D 106 NA NA D2000 1555 1555 2.72 SITE 1 AC1 6 SER C 130 ASP D 101 ASN D 103 THR D 106 SITE 2 AC1 6 GLY D 112 HOH D1056 SITE 1 AC2 4 GLN D 41 GLU D 46 ARG D 47 ARG D 110 SITE 1 AC3 3 ARG E 28 ARG E 29 SER E 30 CRYST1 39.043 59.167 131.425 90.00 92.20 90.00 P 1 21 1 10 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.025613 0.000000 0.000984 0.00000 SCALE2 0.000000 0.016901 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007615 0.00000