HEADER IMMUNE SYSTEM 02-MAR-11 3QXU TITLE FREE STRUCTURE OF AN ANTI-METHOTREXATE CDR1-3 GRAFT VHH ANTIBODY COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTI-METHOTREXATE CDR1-3 GRAFT; COMPND 3 CHAIN: A, B, C, D; 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: PET21A(+) 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, CDR1, KEYWDS 4 CDR4, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR S.W.FANNING,J.R.HORN REVDAT 3 11-SEP-13 3QXU 1 SOURCE REVDAT 2 16-MAY-12 3QXU 1 REMARK VERSN REVDAT 1 06-JUL-11 3QXU 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. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.95 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : NULL 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) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4193 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5857 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.53 REMARK 3 BIN R VALUE (WORKING SET) : 0.2470 REMARK 3 BIN FREE R VALUE SET COUNT : 288 REMARK 3 BIN FREE R VALUE : 0.2620 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3791 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 23 REMARK 3 SOLVENT ATOMS : 378 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.52 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.88000 REMARK 3 B22 (A**2) : 0.88000 REMARK 3 B33 (A**2) : -1.32000 REMARK 3 B12 (A**2) : 0.44000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.087 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.091 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.060 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.206 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.929 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3969 ; 0.030 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5367 ; 1.427 ; 1.935 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 518 ; 7.811 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 176 ;36.465 ;22.500 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 649 ;15.168 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 40 ;20.413 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 565 ; 0.158 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3032 ; 0.014 ; 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): 2490 ; 1.628 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3940 ; 2.671 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1479 ; 3.674 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1412 ; 5.865 ; 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 : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 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 : A 3 A 131 REMARK 3 ORIGIN FOR THE GROUP (A): -40.3260 8.4195 10.3424 REMARK 3 T TENSOR REMARK 3 T11: 0.0315 T22: 0.0111 REMARK 3 T33: 0.0099 T12: -0.0126 REMARK 3 T13: -0.0152 T23: 0.0084 REMARK 3 L TENSOR REMARK 3 L11: 0.8686 L22: 1.3887 REMARK 3 L33: 1.4595 L12: -0.2998 REMARK 3 L13: 0.3122 L23: -0.7070 REMARK 3 S TENSOR REMARK 3 S11: 0.0140 S12: 0.0323 S13: -0.0032 REMARK 3 S21: 0.0341 S22: 0.0359 S23: 0.0349 REMARK 3 S31: 0.0167 S32: 0.0086 S33: -0.0499 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 : B 3 B 131 REMARK 3 ORIGIN FOR THE GROUP (A): -25.2397 32.4007 13.5281 REMARK 3 T TENSOR REMARK 3 T11: 0.0349 T22: 0.0115 REMARK 3 T33: 0.0261 T12: -0.0154 REMARK 3 T13: -0.0065 T23: 0.0117 REMARK 3 L TENSOR REMARK 3 L11: 1.7944 L22: 0.7599 REMARK 3 L33: 1.5940 L12: 0.4607 REMARK 3 L13: -0.4213 L23: 0.0886 REMARK 3 S TENSOR REMARK 3 S11: 0.0392 S12: 0.0563 S13: 0.1613 REMARK 3 S21: 0.0369 S22: -0.0088 S23: 0.0681 REMARK 3 S31: -0.0255 S32: -0.0414 S33: -0.0305 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 3 C 131 REMARK 3 ORIGIN FOR THE GROUP (A): -35.7501 19.3665 -14.0843 REMARK 3 T TENSOR REMARK 3 T11: 0.0508 T22: 0.0504 REMARK 3 T33: 0.0248 T12: -0.0179 REMARK 3 T13: -0.0087 T23: 0.0075 REMARK 3 L TENSOR REMARK 3 L11: 1.5970 L22: 1.2104 REMARK 3 L33: 1.9476 L12: 0.5175 REMARK 3 L13: 0.2671 L23: -0.1875 REMARK 3 S TENSOR REMARK 3 S11: -0.0551 S12: 0.2101 S13: -0.0943 REMARK 3 S21: -0.1827 S22: 0.0258 S23: -0.0421 REMARK 3 S31: 0.0460 S32: 0.0538 S33: 0.0293 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 3 D 131 REMARK 3 ORIGIN FOR THE GROUP (A): -31.8572 23.2215 38.1588 REMARK 3 T TENSOR REMARK 3 T11: 0.0262 T22: 0.0329 REMARK 3 T33: 0.0477 T12: 0.0129 REMARK 3 T13: -0.0061 T23: -0.0323 REMARK 3 L TENSOR REMARK 3 L11: 0.4218 L22: 1.6113 REMARK 3 L33: 1.6225 L12: 0.1790 REMARK 3 L13: 0.1551 L23: 0.3903 REMARK 3 S TENSOR REMARK 3 S11: -0.0084 S12: -0.0511 S13: -0.0084 REMARK 3 S21: 0.1242 S22: 0.1324 S23: -0.1436 REMARK 3 S31: 0.1123 S32: 0.0674 S33: -0.1241 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 3QXU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-MAR-11. REMARK 100 THE RCSB ID CODE IS RCSB064239. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-FEB-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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 : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 91151 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 19.946 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 13.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.13200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.0000 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_MR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.5M SODIUM FORMATE, PH 7.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.28400 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 104.56800 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 78.42600 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 130.71000 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 26.14200 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, 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 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 SER B 31 REMARK 465 ARG B 32 REMARK 465 GLY C 1 REMARK 465 SER C 2 REMARK 465 GLY D 1 REMARK 465 SER D 2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 CB SER A 111 OG SER B 111 2.02 REMARK 500 OE2 GLU C 91 O HOH C 1069 2.07 REMARK 500 CD LYS D 89 OE2 GLU D 91 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU C 8 CD GLU C 8 OE2 -0.097 REMARK 500 REMARK 500 REMARK: NULL 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 94 170.28 177.64 REMARK 500 VAL C 81 146.77 -171.73 REMARK 500 ALA C 94 169.33 175.06 REMARK 500 ASN D 79 56.71 -96.31 REMARK 500 ALA D 94 164.98 176.68 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 SER B 33 TRP B 34 149.97 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 A1004 DISTANCE = 6.67 ANGSTROMS REMARK 525 HOH A1005 DISTANCE = 5.81 ANGSTROMS REMARK 525 HOH D1051 DISTANCE = 6.30 ANGSTROMS REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 FMT D 2001 REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 HOH A 1018 REMARK 615 HOH D 1009 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 2000 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 2001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 2002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT B 2000 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT B 2002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT B 2004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT D 2001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT D 2000 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 REMARK 900 WITH THE DYE RR1 REMARK 900 RELATED ID: 2X6M RELATED DB: PDB REMARK 900 STRUCTURE OF A SINGLE DOMAIN CAMELID ANTIBODY FRAGMENT IN REMARK 900 COMPLEX WITH A C-TERMINAL PEPTIDE OF ALPHA-SYNUCLEIN DBREF 3QXU A 1 131 PDB 3QXU 3QXU 1 131 DBREF 3QXU B 1 131 PDB 3QXU 3QXU 1 131 DBREF 3QXU C 1 131 PDB 3QXU 3QXU 1 131 DBREF 3QXU D 1 131 PDB 3QXU 3QXU 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 LYS GLY LYS SEQRES 7 A 126 ASN THR 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 LYS GLY LYS SEQRES 7 B 126 ASN THR 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 LYS GLY LYS SEQRES 7 C 126 ASN THR 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 LYS GLY LYS SEQRES 7 D 126 ASN THR 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 HET FMT A2000 3 HET FMT A2001 3 HET FMT A2002 3 HET FMT B2000 3 HET FMT B2002 3 HET FMT B2004 3 HET FMT D2001 2 HET FMT D2000 3 HETNAM FMT FORMIC ACID FORMUL 5 FMT 8(C H2 O2) FORMUL 13 HOH *378(H2 O) HELIX 1 1 LYS A 89 THR A 93 5 5 HELIX 2 2 TYR A 104 TRP A 109 5 6 HELIX 3 3 ASP B 64 LYS B 67 5 4 HELIX 4 4 LYS B 89 THR B 93 5 5 HELIX 5 5 VAL B 105 TRP B 109 5 5 HELIX 6 6 LYS C 89 THR C 93 5 5 HELIX 7 7 LYS D 89 THR D 93 5 5 HELIX 8 8 VAL D 105 TRP D 109 5 5 SHEET 1 A 4 LEU A 6 SER A 9 0 SHEET 2 A 4 LEU A 20 ALA A 26 -1 O SER A 23 N SER A 9 SHEET 3 A 4 THR A 80 MET A 85 -1 O MET A 85 N LEU A 20 SHEET 4 A 4 PHE A 70 SER A 73 -1 N THR A 71 O GLN A 84 SHEET 1 B 6 GLY A 12 GLN A 15 0 SHEET 2 B 6 THR A 125 SER A 130 1 O SER A 130 N VAL A 14 SHEET 3 B 6 ALA A 94 ASP A 101 -1 N ALA A 94 O VAL A 127 SHEET 4 B 6 ALA A 35 GLN A 41 -1 N PHE A 39 O TYR A 97 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 SER A 130 N VAL A 14 SHEET 3 C 4 ALA A 94 ASP A 101 -1 N ALA A 94 O VAL A 127 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 THR B 80 MET B 85 -1 O MET B 85 N LEU B 20 SHEET 4 D 4 PHE B 70 ARG B 74 -1 N THR B 71 O GLN B 84 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 ALA B 42 -1 N PHE B 39 O TYR B 97 SHEET 5 E 6 LYS B 45 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 C 6 SER C 9 0 SHEET 2 G 4 LEU C 20 ALA C 26 -1 O SER C 23 N SER C 9 SHEET 3 G 4 THR C 80 MET C 85 -1 O MET C 85 N LEU C 20 SHEET 4 G 4 PHE C 70 SER C 73 -1 N THR C 71 O GLN C 84 SHEET 1 H 6 GLY C 12 GLN C 15 0 SHEET 2 H 6 THR C 125 SER C 130 1 O THR C 128 N GLY C 12 SHEET 3 H 6 ALA C 94 ASP C 101 -1 N TYR C 96 O THR C 125 SHEET 4 H 6 ALA C 35 GLN C 41 -1 N PHE C 39 O TYR C 97 SHEET 5 H 6 GLU C 48 ILE C 53 -1 O GLU C 48 N ARG C 40 SHEET 6 H 6 THR C 60 TYR C 62 -1 O THR C 61 N LYS C 52 SHEET 1 I 4 GLY C 12 GLN C 15 0 SHEET 2 I 4 THR C 125 SER C 130 1 O THR C 128 N GLY C 12 SHEET 3 I 4 ALA C 94 ASP C 101 -1 N TYR C 96 O THR C 125 SHEET 4 I 4 TYR C 120 TRP C 121 -1 O TYR C 120 N ALA C 100 SHEET 1 J 4 LEU D 6 SER D 9 0 SHEET 2 J 4 LEU D 20 ALA D 26 -1 O ALA D 25 N VAL D 7 SHEET 3 J 4 THR D 80 MET D 85 -1 O MET D 85 N LEU D 20 SHEET 4 J 4 PHE D 70 ARG D 74 -1 N THR D 71 O GLN D 84 SHEET 1 K 6 GLY D 12 GLN D 15 0 SHEET 2 K 6 THR D 125 SER D 130 1 O THR D 128 N VAL D 14 SHEET 3 K 6 ALA D 94 ASP D 101 -1 N TYR D 96 O THR D 125 SHEET 4 K 6 ALA D 35 GLN D 41 -1 N GLN D 41 O VAL D 95 SHEET 5 K 6 GLU D 48 ILE D 53 -1 O ALA D 51 N TRP D 38 SHEET 6 K 6 THR D 60 TYR D 62 -1 O THR D 61 N LYS D 52 SHEET 1 L 4 GLY D 12 GLN D 15 0 SHEET 2 L 4 THR D 125 SER D 130 1 O THR D 128 N VAL D 14 SHEET 3 L 4 ALA D 94 ASP D 101 -1 N TYR D 96 O THR D 125 SHEET 4 L 4 TYR D 120 TRP D 121 -1 O TYR D 120 N ALA D 100 SSBOND 1 CYS A 24 CYS A 98 1555 1555 2.25 SSBOND 2 CYS B 24 CYS B 98 1555 1555 2.21 SSBOND 3 CYS C 24 CYS C 98 1555 1555 2.07 SSBOND 4 CYS D 24 CYS D 98 1555 1555 2.08 SITE 1 AC1 8 SER A 54 GLY A 55 ASN A 103 TYR A 104 SITE 2 AC1 8 HOH A1059 FMT A2001 GLN C 41 HOH C1053 SITE 1 AC2 6 ARG A 32 SER A 33 HOH A1058 HOH A1103 SITE 2 AC2 6 HOH A1106 FMT A2000 SITE 1 AC3 6 GLN B 126 HOH B1043 VAL C 14 GLN C 15 SITE 2 AC3 6 SER C 130 HOH C1073 SITE 1 AC4 7 ASP B 102 ASN B 103 TYR B 104 HOH B1046 SITE 2 AC4 7 FMT B2004 GLN D 41 ARG D 110 SITE 1 AC5 5 ARG B 47 ARG B 110 TRP B 121 HOH B1018 SITE 2 AC5 5 HOH B1042 SITE 1 AC6 7 SER B 33 ALA B 35 SER B 54 GLY B 55 SITE 2 AC6 7 TYR B 104 HOH B1002 FMT B2000 SITE 1 AC7 6 ASP C 101 ASN C 103 THR C 106 GLY C 112 SITE 2 AC7 6 HOH C1037 FMT D2000 SITE 1 AC8 3 SER D 111 HOH D1068 FMT D2001 CRYST1 101.087 101.087 156.852 90.00 90.00 120.00 P 61 24 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 0.009892 0.005711 0.000000 0.00000 SCALE2 0.000000 0.011423 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006375 0.00000