HEADER IMMUNE SYSTEM 02-MAR-11 3QXT TITLE STRUCTURE OF AN ANTI-METHOTREXATE CDR1-3 GRAFT VHH ANTIBODY IN COMPLEX TITLE 2 WITH METHOTREXATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTI-METHOTREXATE CDR1-3 GRAFT VHH; COMPND 3 CHAIN: A, B; 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, IMMUNE KEYWDS 4 SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR S.W.FANNING,J.R.HORN REVDAT 2 11-SEP-13 3QXT 1 SOURCE VERSN REVDAT 1 06-JUL-11 3QXT 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. 1.70 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 3 NUMBER OF REFLECTIONS : 50174 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) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2698 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2582 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 68.39 REMARK 3 BIN R VALUE (WORKING SET) : 0.2940 REMARK 3 BIN FREE R VALUE SET COUNT : 140 REMARK 3 BIN FREE R VALUE : 0.2870 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1904 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 71 REMARK 3 SOLVENT ATOMS : 222 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.09 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.03000 REMARK 3 B22 (A**2) : 1.03000 REMARK 3 B33 (A**2) : -1.55000 REMARK 3 B12 (A**2) : 0.52000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.072 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.047 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.172 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.960 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2050 ; 0.033 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 4 ; 0.008 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2781 ; 2.499 ; 1.974 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10 ; 2.043 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 258 ; 5.517 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 88 ;36.992 ;22.500 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 323 ;15.082 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;18.669 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 284 ; 0.329 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1584 ; 0.015 ; 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): 1247 ; 1.811 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1989 ; 3.014 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 803 ; 4.484 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 785 ; 6.569 ; 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 : 2 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): 26.6413 -32.4740 -11.2813 REMARK 3 T TENSOR REMARK 3 T11: 0.0213 T22: 0.0606 REMARK 3 T33: 0.0267 T12: -0.0170 REMARK 3 T13: -0.0134 T23: -0.0079 REMARK 3 L TENSOR REMARK 3 L11: 1.0127 L22: 0.1693 REMARK 3 L33: 1.1432 L12: -0.1427 REMARK 3 L13: 0.8640 L23: -0.0240 REMARK 3 S TENSOR REMARK 3 S11: -0.0045 S12: 0.0329 S13: -0.0446 REMARK 3 S21: 0.0115 S22: 0.0141 S23: 0.0107 REMARK 3 S31: -0.0513 S32: 0.0473 S33: -0.0096 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): 33.5174 -22.4116 13.6691 REMARK 3 T TENSOR REMARK 3 T11: 0.0785 T22: 0.0122 REMARK 3 T33: 0.0260 T12: -0.0237 REMARK 3 T13: -0.0239 T23: 0.0067 REMARK 3 L TENSOR REMARK 3 L11: 0.5629 L22: 0.4364 REMARK 3 L33: 1.3389 L12: 0.2284 REMARK 3 L13: 0.0654 L23: -0.0093 REMARK 3 S TENSOR REMARK 3 S11: 0.0222 S12: -0.0109 S13: -0.0130 REMARK 3 S21: 0.1077 S22: -0.0060 S23: -0.0050 REMARK 3 S31: 0.0450 S32: -0.0439 S33: -0.0162 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 3QXT 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 RCSB064238. 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 : 52887 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.900 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 200 DATA REDUNDANCY : 10.800 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 34.4000 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 (%): 72.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0M SUCCINIC ACID, 0.1M HEPES, 1% W/V REMARK 280 PEG 2,000, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 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 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-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 52.35767 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 104.71533 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 78.53650 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 130.89417 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 26.17883 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 52.35767 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 104.71533 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 130.89417 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 78.53650 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 26.17883 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 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 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 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 PRO A 43 C PRO A 43 O 0.134 REMARK 500 GLU A 48 CG GLU A 48 CD 0.093 REMARK 500 VAL A 81 CB VAL A 81 CG2 -0.128 REMARK 500 GLN A 126 CB GLN A 126 CG -0.200 REMARK 500 VAL B 81 CB VAL B 81 CG2 -0.139 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 ASP A 102 CB - CG - OD1 ANGL. DEV. = 8.3 DEGREES REMARK 500 ARG A 110 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG B 47 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 ASP B 102 CB - CG - OD1 ANGL. DEV. = 8.1 DEGREES 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 94 167.86 179.85 REMARK 500 ALA B 94 166.25 178.17 REMARK 500 REMARK 500 REMARK: NULL 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 A 133 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 101 OD1 REMARK 620 2 ASP A 102 OD1 82.1 REMARK 620 3 ASP A 119 OD1 92.5 77.5 REMARK 620 4 GLY A 112 O 89.7 166.0 91.6 REMARK 620 5 HOH A1066 O 171.9 104.8 84.9 82.7 REMARK 620 6 HOH A1018 O 90.7 101.0 176.2 90.3 92.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 132 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 101 OD1 REMARK 620 2 ASP B 102 OD1 83.3 REMARK 620 3 ASP B 119 OD1 95.4 85.6 REMARK 620 4 GLY B 112 O 89.1 172.3 96.7 REMARK 620 5 HOH B1044 O 164.1 110.5 93.7 76.8 REMARK 620 6 HOH B1087 O 88.5 88.7 172.6 89.6 84.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 133 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER B 111 O REMARK 620 2 GLY B 112 O 88.0 REMARK 620 3 HOH B1044 O 169.4 81.8 REMARK 620 4 HOH B1083 O 86.3 92.9 91.3 REMARK 620 5 HOH B1055 O 88.2 102.2 96.8 163.8 REMARK 620 6 HOH B1017 O 55.9 124.4 128.8 49.5 115.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 132 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG A 74 O REMARK 620 2 HOH A1106 O 85.0 REMARK 620 3 HOH A1120 O 89.4 82.8 REMARK 620 4 HOH A1098 O 176.4 92.5 92.8 REMARK 620 5 HOH A1026 O 87.4 95.3 176.4 90.3 REMARK 620 6 HOH A1023 O 90.2 172.9 92.0 92.6 89.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 134 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG B 74 O REMARK 620 2 HOH B1018 O 91.1 REMARK 620 3 HOH B1075 O 79.9 83.6 REMARK 620 4 HOH B1048 O 93.6 97.8 173.4 REMARK 620 5 HOH B1034 O 83.8 173.6 91.8 86.3 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MTX A 2000 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 132 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 133 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MTX B 2000 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 132 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 133 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 134 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 REMARK 900 RELATED ID: 3QXU RELATED DB: PDB REMARK 900 RELATED ID: 3QXV RELATED DB: PDB REMARK 900 RELATED ID: 3QXW RELATED DB: PDB DBREF 3QXT A 1 131 PDB 3QXT 3QXT 1 131 DBREF 3QXT B 1 131 PDB 3QXT 3QXT 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 HET MTX A2000 33 HET NA A 132 1 HET NA A 133 1 HET MTX B2000 33 HET NA B 132 1 HET NA B 133 1 HET NA B 134 1 HETNAM MTX METHOTREXATE HETNAM NA SODIUM ION FORMUL 3 MTX 2(C20 H22 N8 O5) FORMUL 4 NA 5(NA 1+) FORMUL 10 HOH *222(H2 O) HELIX 1 1 LYS A 89 THR A 93 5 5 HELIX 2 2 VAL A 105 TRP A 109 5 5 HELIX 3 3 LYS B 89 THR B 93 5 5 HELIX 4 4 TYR B 104 TRP B 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 THR 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 SER A 73 O TYR A 82 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 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 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 ALA B 25 N VAL B 7 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 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 GLY B 12 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 GLN B 41 O VAL B 95 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 GLY B 12 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 SSBOND 1 CYS A 24 CYS A 98 1555 1555 2.17 SSBOND 2 CYS B 24 CYS B 98 1555 1555 2.13 LINK OD1 ASP A 101 NA NA A 133 1555 1555 2.21 LINK OD1 ASP B 101 NA NA B 132 1555 1555 2.26 LINK OD1 ASP B 102 NA NA B 132 1555 1555 2.30 LINK O SER B 111 NA NA B 133 1555 1555 2.37 LINK O ARG A 74 NA NA A 132 1555 1555 2.38 LINK OD1 ASP B 119 NA NA B 132 1555 1555 2.42 LINK O GLY B 112 NA NA B 133 1555 1555 2.46 LINK O ARG B 74 NA NA B 134 1555 1555 2.48 LINK O GLY B 112 NA NA B 132 1555 1555 2.55 LINK OD1 ASP A 102 NA NA A 133 1555 1555 2.56 LINK OD1 ASP A 119 NA NA A 133 1555 1555 2.64 LINK O GLY A 112 NA NA A 133 1555 1555 2.89 LINK NA NA B 133 O HOH B1044 1555 1555 2.26 LINK NA NA B 133 O HOH B1083 1555 1555 2.30 LINK NA NA A 133 O HOH A1066 1555 1555 2.34 LINK NA NA A 133 O HOH A1018 1555 1555 2.35 LINK NA NA A 132 O HOH A1106 1555 1555 2.35 LINK NA NA A 132 O HOH A1120 1555 1555 2.39 LINK NA NA B 132 O HOH B1044 1555 1555 2.44 LINK NA NA B 134 O HOH B1018 1555 1555 2.45 LINK NA NA A 132 O HOH A1098 1555 1555 2.47 LINK NA NA A 132 O HOH A1026 1555 1555 2.55 LINK NA NA B 134 O HOH B1075 1555 1555 2.56 LINK NA NA B 132 O HOH B1087 1555 1555 2.58 LINK NA NA B 134 O HOH B1048 1555 1555 2.64 LINK NA NA B 133 O HOH B1055 1555 1555 2.67 LINK NA NA B 134 O HOH B1034 1555 1555 2.69 LINK NA NA A 132 O HOH A1023 1555 1555 2.78 LINK NA NA B 133 O HOH B1017 1555 1555 3.07 SITE 1 AC1 19 VAL A 4 CYS A 24 ALA A 26 ARG A 28 SITE 2 AC1 19 ARG A 29 SER A 30 SER A 31 ARG A 32 SITE 3 AC1 19 TRP A 34 ARG A 74 ASP A 75 ASN A 79 SITE 4 AC1 19 THR A 80 VAL A 81 ALA A 100 HOH A1005 SITE 5 AC1 19 HOH A1064 HOH A1118 ARG B 58 SITE 1 AC2 6 ARG A 74 HOH A1023 HOH A1026 HOH A1098 SITE 2 AC2 6 HOH A1106 HOH A1120 SITE 1 AC3 6 ASP A 101 ASP A 102 GLY A 112 ASP A 119 SITE 2 AC3 6 HOH A1018 HOH A1066 SITE 1 AC4 17 VAL B 4 CYS B 24 ALA B 26 ARG B 28 SITE 2 AC4 17 ARG B 29 SER B 30 SER B 31 ARG B 32 SITE 3 AC4 17 TRP B 34 MET B 36 ARG B 74 ASP B 75 SITE 4 AC4 17 ASN B 79 THR B 80 VAL B 81 ALA B 100 SITE 5 AC4 17 HOH B1022 SITE 1 AC5 7 ASP B 101 ASP B 102 GLY B 112 ASP B 119 SITE 2 AC5 7 NA B 133 HOH B1044 HOH B1087 SITE 1 AC6 7 SER B 111 GLY B 112 NA B 132 HOH B1017 SITE 2 AC6 7 HOH B1044 HOH B1055 HOH B1083 SITE 1 AC7 5 ARG B 74 HOH B1018 HOH B1034 HOH B1048 SITE 2 AC7 5 HOH B1075 CRYST1 103.063 103.063 157.073 90.00 90.00 120.00 P 61 2 2 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 0.009703 0.005602 0.000000 0.00000 SCALE2 0.000000 0.011204 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006366 0.00000