HEADER DE NOVO PROTEIN, IMMUNE SYSTEM 04-MAY-11 3RU8 TITLE STRUCTURE OF AN HIV EPITOPE SCAFFOLD IN COMPLEX WITH NEUTRALIZING TITLE 2 ANTIBODY B12 FAB COMPND MOL_ID: 1; COMPND 2 MOLECULE: EPITOPE SCAFFOLD 2BODX43; COMPND 3 CHAIN: X; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: ANTIBODY B12, HEAVY CHAIN; COMPND 7 CHAIN: H; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: ANTIBODY B12, LIGHT CHAIN; COMPND 11 CHAIN: L; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS, SYNTHETIC SOURCE 3 CONSTRUCT, THERMOMONOSPORA FUSCA; SOURCE 4 ORGANISM_TAXID: 12721, 32630, 2021; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET29; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 15 MOL_ID: 3; SOURCE 16 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 17 ORGANISM_COMMON: HUMAN; SOURCE 18 ORGANISM_TAXID: 9606; SOURCE 19 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 20 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS BINDING EPITOPE FROM HIV ON A HETEROLOGOUS PROTEIN, IMMUNE SYSTEM, DE KEYWDS 2 NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.T.D.CARRICO,R.K.STRONG REVDAT 5 13-SEP-23 3RU8 1 REMARK REVDAT 4 08-NOV-17 3RU8 1 REMARK REVDAT 3 22-FEB-12 3RU8 1 JRNL SOURCE REVDAT 2 07-DEC-11 3RU8 1 REMARK REVDAT 1 02-NOV-11 3RU8 0 JRNL AUTH M.L.AZOITEI,B.E.CORREIA,Y.E.BAN,C.CARRICO,O.KALYUZHNIY, JRNL AUTH 2 L.CHEN,A.SCHROETER,P.S.HUANG,J.S.MCLELLAN,P.D.KWONG,D.BAKER, JRNL AUTH 3 R.K.STRONG,W.R.SCHIEF JRNL TITL COMPUTATION-GUIDED BACKBONE GRAFTING OF A DISCONTINUOUS JRNL TITL 2 MOTIF ONTO A PROTEIN SCAFFOLD. JRNL REF SCIENCE V. 334 373 2011 JRNL REFN ISSN 0036-8075 JRNL PMID 22021856 JRNL DOI 10.1126/SCIENCE.1209368 REMARK 2 REMARK 2 RESOLUTION. 2.07 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 2.07 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.23 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 48971 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) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2485 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) : 2.07 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.12 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3201 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.57 REMARK 3 BIN R VALUE (WORKING SET) : 0.1760 REMARK 3 BIN FREE R VALUE SET COUNT : 178 REMARK 3 BIN FREE R VALUE : 0.2080 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5372 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 24 REMARK 3 SOLVENT ATOMS : 343 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.27 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.06000 REMARK 3 B22 (A**2) : -0.03000 REMARK 3 B33 (A**2) : -0.03000 REMARK 3 B12 (A**2) : 0.00000 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): 0.152 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.097 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.774 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5699 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 3806 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7805 ; 1.166 ; 1.939 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9294 ; 0.805 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 763 ; 5.906 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 245 ;33.898 ;23.796 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 857 ;12.588 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 36 ;20.392 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 853 ; 0.072 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6527 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1170 ; 0.001 ; 0.020 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): 3638 ; 0.718 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1468 ; 0.170 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5873 ; 1.330 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2061 ; 2.021 ; 4.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1905 ; 3.120 ; 6.000 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 : 6 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 : X 1 X 140 REMARK 3 ORIGIN FOR THE GROUP (A): -5.0856 -0.6088 -22.3595 REMARK 3 T TENSOR REMARK 3 T11: 0.0862 T22: 0.1621 REMARK 3 T33: 0.1220 T12: 0.0232 REMARK 3 T13: 0.0222 T23: 0.0069 REMARK 3 L TENSOR REMARK 3 L11: 1.5636 L22: 2.2081 REMARK 3 L33: 1.1706 L12: 0.7861 REMARK 3 L13: 0.0327 L23: -0.9186 REMARK 3 S TENSOR REMARK 3 S11: -0.0030 S12: 0.0290 S13: 0.1326 REMARK 3 S21: 0.1677 S22: -0.0143 S23: 0.0664 REMARK 3 S31: -0.1501 S32: -0.0789 S33: 0.0173 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 : X 141 X 277 REMARK 3 ORIGIN FOR THE GROUP (A): 1.2868 -14.4141 -23.5758 REMARK 3 T TENSOR REMARK 3 T11: 0.0895 T22: 0.1785 REMARK 3 T33: 0.2244 T12: 0.0081 REMARK 3 T13: 0.0525 T23: 0.0229 REMARK 3 L TENSOR REMARK 3 L11: 1.9176 L22: 1.5674 REMARK 3 L33: 1.3872 L12: 0.4984 REMARK 3 L13: 0.1425 L23: -0.3894 REMARK 3 S TENSOR REMARK 3 S11: -0.0444 S12: 0.0747 S13: -0.2822 REMARK 3 S21: -0.0593 S22: -0.0702 S23: -0.2914 REMARK 3 S31: 0.1107 S32: 0.0634 S33: 0.1147 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 : H 1 H 126 REMARK 3 ORIGIN FOR THE GROUP (A): -19.3226 -18.2903 4.6533 REMARK 3 T TENSOR REMARK 3 T11: 0.0910 T22: 0.1781 REMARK 3 T33: 0.2063 T12: 0.0023 REMARK 3 T13: 0.0509 T23: 0.0230 REMARK 3 L TENSOR REMARK 3 L11: 1.2028 L22: 0.8351 REMARK 3 L33: 3.5072 L12: -0.2201 REMARK 3 L13: -0.3760 L23: 0.1618 REMARK 3 S TENSOR REMARK 3 S11: 0.0549 S12: 0.0015 S13: 0.0611 REMARK 3 S21: 0.0110 S22: 0.1120 S23: 0.0579 REMARK 3 S31: -0.1527 S32: -0.1412 S33: -0.1669 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 : H 127 H 227 REMARK 3 ORIGIN FOR THE GROUP (A): 4.1547 -17.7098 31.8394 REMARK 3 T TENSOR REMARK 3 T11: 0.0801 T22: 0.1261 REMARK 3 T33: 0.0940 T12: 0.0122 REMARK 3 T13: 0.0248 T23: -0.0731 REMARK 3 L TENSOR REMARK 3 L11: 7.7299 L22: 1.3082 REMARK 3 L33: 2.3186 L12: -0.7974 REMARK 3 L13: 1.2778 L23: 0.3005 REMARK 3 S TENSOR REMARK 3 S11: -0.0308 S12: -0.3003 S13: 0.3562 REMARK 3 S21: 0.0352 S22: -0.0188 S23: -0.1248 REMARK 3 S31: -0.2343 S32: -0.0310 S33: 0.0496 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 : L 1 L 107 REMARK 3 ORIGIN FOR THE GROUP (A): -5.5924 -34.6871 0.3340 REMARK 3 T TENSOR REMARK 3 T11: 0.0712 T22: 0.1427 REMARK 3 T33: 0.1353 T12: -0.0020 REMARK 3 T13: 0.0231 T23: -0.0241 REMARK 3 L TENSOR REMARK 3 L11: 2.1458 L22: 1.8277 REMARK 3 L33: 2.7152 L12: -0.6036 REMARK 3 L13: -0.1723 L23: 0.2296 REMARK 3 S TENSOR REMARK 3 S11: -0.0555 S12: 0.0102 S13: -0.0825 REMARK 3 S21: 0.0744 S22: 0.1442 S23: -0.0255 REMARK 3 S31: 0.0546 S32: 0.0707 S33: -0.0887 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : L 108 L 213 REMARK 3 ORIGIN FOR THE GROUP (A): 3.4869 -33.5077 34.4232 REMARK 3 T TENSOR REMARK 3 T11: 0.1959 T22: 0.1919 REMARK 3 T33: 0.0769 T12: 0.0741 REMARK 3 T13: -0.0034 T23: -0.0047 REMARK 3 L TENSOR REMARK 3 L11: 2.1741 L22: 1.5844 REMARK 3 L33: 9.7496 L12: -0.7838 REMARK 3 L13: -3.0120 L23: 3.5447 REMARK 3 S TENSOR REMARK 3 S11: -0.1639 S12: -0.3017 S13: -0.1479 REMARK 3 S21: 0.4951 S22: 0.0554 S23: 0.0674 REMARK 3 S31: 0.9834 S32: 0.2491 S33: 0.1085 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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 3RU8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-MAY-11. REMARK 100 THE DEPOSITION ID IS D_1000065383. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JUL-10 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49114 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.070 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.10300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.07 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.3 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : 0.34000 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 2.1.4 REMARK 200 STARTING MODEL: PDB ENTRIES 2BOD, 2NY7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% PEG-3350, 0.22M POTASSIUM NITRATE, REMARK 280 PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 45.22650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.18650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.54850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.18650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 45.22650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 46.54850 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6770 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: X, H, L 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 HIS X 278 REMARK 465 HIS X 279 REMARK 465 HIS X 280 REMARK 465 HIS X 281 REMARK 465 HIS X 282 REMARK 465 LYS H 131 REMARK 465 SER H 132 REMARK 465 LYS H 228 REMARK 465 SER H 229 REMARK 465 CYS H 230 REMARK 465 GLU L 214 REMARK 465 CYS L 215 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN X 48 CG CD OE1 NE2 REMARK 470 GLN X 81 CG CD OE1 NE2 REMARK 470 GLU X 84 CG CD OE1 OE2 REMARK 470 HIS X 277 CG ND1 CD2 CE1 NE2 REMARK 470 GLN H 1 CG CD OE1 NE2 REMARK 470 LYS H 213 CG CD CE NZ REMARK 470 LYS H 218 CG CD CE NZ REMARK 470 GLU L 1 CG CD OE1 OE2 REMARK 470 ARG L 24 NE CZ NH1 NH2 REMARK 470 ARG L 30 CG CD NE CZ NH1 NH2 REMARK 470 SER L 57 OG REMARK 470 LYS L 146 CG CD CE NZ REMARK 470 LEU L 155 CG CD1 CD2 REMARK 470 LYS L 170 CG CD CE NZ REMARK 470 LYS L 189 CG CD CE NZ REMARK 470 ARG L 203 CG CD NE CZ NH1 NH2 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 ILE X 32 -54.00 -122.41 REMARK 500 ALA X 102 144.72 -175.44 REMARK 500 TRP X 150 -111.59 -138.02 REMARK 500 ASN X 178 -163.15 -111.81 REMARK 500 GLN H 100E -0.71 75.48 REMARK 500 VAL L 52 -46.70 75.25 REMARK 500 ALA L 85 175.34 173.88 REMARK 500 SER L 95 13.94 59.19 REMARK 500 LYS L 191 -60.73 -104.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL L 216 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL X 283 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL L 217 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL X 284 REMARK 999 REMARK 999 SEQUENCE REMARK 999 EPITOPE SCAFFOLD 2BODX43 INCORPORATES A SMALL SECTION OF HIV-1 REMARK 999 GP120 INTO A PROTEIN FROM THERMOMONOSPORA FUSCA, PLUS SOME DESIGNED REMARK 999 REGIONS NATIVE TO NEITHER ORGANISM. THE CLOSER MATCH WITH THE REMARK 999 CRYSTALLIZED SEQUENCE OF THIS CHAIN CORRESPONDS TO UNP ENTRY P26222. DBREF 3RU8 X 1 282 PDB 3RU8 3RU8 1 282 DBREF 3RU8 H 1 230 PDB 3RU8 3RU8 1 230 DBREF 3RU8 L 1 215 PDB 3RU8 3RU8 1 215 SEQRES 1 X 282 ASP SER PRO PHE TYR VAL ASN PRO ASN MET SER SER ALA SEQRES 2 X 282 GLU TRP VAL ARG ASN ASN PRO ASN ASP PRO ARG THR PRO SEQRES 3 X 282 VAL ILE ARG ASN ARG ILE ALA SER VAL PRO GLN GLY THR SEQRES 4 X 282 TRP HIS ASN GLN HIS ASN PRO GLY GLN ILE THR GLY GLN SEQRES 5 X 282 VAL ASP ALA LEU MET SER ALA ALA GLN ALA ALA GLY LYS SEQRES 6 X 282 ILE PRO ILE LEU VAL VAL ASP VAL GLY PRO THR GLY ASP SEQRES 7 X 282 MET SER GLN GLY GLU GLU ALA GLY LYS GLN TRP ILE ASP SEQRES 8 X 282 GLU PHE ALA ALA GLY LEU LYS ASN ARG PRO ALA TYR ILE SEQRES 9 X 282 ILE VAL TYR PRO LEU TYR SER GLY GLY ASP PRO GLU ILE SEQRES 10 X 282 VAL GLN GLU TRP LEU ARG THR VAL ALA TYR ALA GLY LYS SEQRES 11 X 282 ALA LEU LYS ALA GLY SER SER GLN ALA ARG ILE TYR PHE SEQRES 12 X 282 ASP ALA GLY HIS SER ALA TRP HIS SER PRO ALA GLN MET SEQRES 13 X 282 ALA ALA ALA LEU GLN ARG ALA ASP ILE SER ASN SER ALA SEQRES 14 X 282 HIS GLY ILE ALA THR ASN THR SER ASN TYR ARG TRP THR SEQRES 15 X 282 ALA ASP GLU VAL ALA TYR ALA LYS ALA VAL LEU SER ALA SEQRES 16 X 282 ILE GLY ASN PRO SER LEU ARG ALA VAL ILE ASP THR SER SEQRES 17 X 282 ARG ASN GLY ASN GLY PRO ALA GLY ASN GLU SER CYS ASP SEQRES 18 X 282 PRO SER GLY ARG ALA ILE GLY THR PRO SER THR THR ASN SEQRES 19 X 282 THR GLY ASP PRO MET ILE ASP ALA PHE LEU TRP ILE LYS SEQRES 20 X 282 LEU PRO GLY GLU ALA ASP GLY CYS ILE ALA GLY ALA GLY SEQRES 21 X 282 GLN PHE VAL PRO GLN ALA ALA TYR GLU MET ALA ILE ALA SEQRES 22 X 282 ALA LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 H 230 GLN VAL GLN LEU VAL GLN SER GLY ALA GLU VAL LYS LYS SEQRES 2 H 230 PRO GLY ALA SER VAL LYS VAL SER CYS GLN ALA SER GLY SEQRES 3 H 230 TYR ARG PHE SER ASN PHE VAL ILE HIS TRP VAL ARG GLN SEQRES 4 H 230 ALA PRO GLY GLN ARG PHE GLU TRP MET GLY TRP ILE ASN SEQRES 5 H 230 PRO TYR ASN GLY ASN LYS GLU PHE SER ALA LYS PHE GLN SEQRES 6 H 230 ASP ARG VAL THR PHE THR ALA ASP THR SER ALA ASN THR SEQRES 7 H 230 ALA TYR MET GLU LEU ARG SER LEU ARG SER ALA ASP THR SEQRES 8 H 230 ALA VAL TYR TYR CYS ALA ARG VAL GLY PRO TYR SER TRP SEQRES 9 H 230 ASP ASP SER PRO GLN ASP ASN TYR TYR MET ASP VAL TRP SEQRES 10 H 230 GLY LYS GLY THR THR VAL ILE VAL SER SER ALA SER THR SEQRES 11 H 230 LYS GLY PRO SER VAL PHE PRO LEU ALA PRO SER SER LYS SEQRES 12 H 230 SER THR SER GLY GLY THR ALA ALA LEU GLY CYS LEU VAL SEQRES 13 H 230 LYS ASP TYR PHE PRO GLU PRO VAL THR VAL SER TRP ASN SEQRES 14 H 230 SER GLY ALA LEU THR SER GLY VAL HIS THR PHE PRO ALA SEQRES 15 H 230 VAL LEU GLN SER SER GLY LEU TYR SER LEU SER SER VAL SEQRES 16 H 230 VAL THR VAL PRO SER SER SER LEU GLY THR GLN THR TYR SEQRES 17 H 230 ILE CYS ASN VAL ASN HIS LYS PRO SER ASN THR LYS VAL SEQRES 18 H 230 ASP LYS LYS VAL GLU PRO LYS SER CYS SEQRES 1 L 215 GLU ILE VAL LEU THR GLN SER PRO GLY THR LEU SER LEU SEQRES 2 L 215 SER PRO GLY GLU ARG ALA THR PHE SER CYS ARG SER SER SEQRES 3 L 215 HIS SER ILE ARG SER ARG ARG VAL ALA TRP TYR GLN HIS SEQRES 4 L 215 LYS PRO GLY GLN ALA PRO ARG LEU VAL ILE HIS GLY VAL SEQRES 5 L 215 SER ASN ARG ALA SER GLY ILE SER ASP ARG PHE SER GLY SEQRES 6 L 215 SER GLY SER GLY THR ASP PHE THR LEU THR ILE THR ARG SEQRES 7 L 215 VAL GLU PRO GLU ASP PHE ALA LEU TYR TYR CYS GLN VAL SEQRES 8 L 215 TYR GLY ALA SER SER TYR THR PHE GLY GLN GLY THR LYS SEQRES 9 L 215 LEU GLU ARG LYS ARG THR VAL ALA ALA PRO SER VAL PHE SEQRES 10 L 215 ILE PHE PRO PRO SER ASP GLU GLN LEU LYS SER GLY THR SEQRES 11 L 215 ALA SER VAL VAL CYS LEU LEU ASN ASN PHE TYR PRO ARG SEQRES 12 L 215 GLU ALA LYS VAL GLN TRP LYS VAL ASP ASN ALA LEU GLN SEQRES 13 L 215 SER GLY ASN SER GLN GLU SER VAL THR GLU GLN ASP SER SEQRES 14 L 215 LYS ASP SER THR TYR SER LEU SER SER THR LEU THR LEU SEQRES 15 L 215 SER LYS ALA ASP TYR GLU LYS HIS LYS VAL TYR ALA CYS SEQRES 16 L 215 GLU VAL THR HIS GLN GLY LEU ARG SER PRO VAL THR LYS SEQRES 17 L 215 SER PHE ASN ARG GLY GLU CYS HET GOL X 283 6 HET GOL X 284 6 HET GOL L 216 6 HET GOL L 217 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 4 GOL 4(C3 H8 O3) FORMUL 8 HOH *343(H2 O) HELIX 1 1 MET X 10 ASN X 19 1 10 HELIX 2 2 ARG X 24 ILE X 32 1 9 HELIX 3 3 GLN X 48 GLY X 64 1 17 HELIX 4 4 GLY X 82 GLY X 96 1 15 HELIX 5 5 ASP X 114 SER X 136 1 23 HELIX 6 6 SER X 152 ALA X 163 1 12 HELIX 7 7 ASP X 164 ALA X 169 1 6 HELIX 8 8 TRP X 181 GLY X 197 1 17 HELIX 9 9 VAL X 263 GLU X 276 1 14 HELIX 10 10 ARG H 28 PHE H 32 5 5 HELIX 11 11 THR H 73 ALA H 75 5 3 HELIX 12 12 ARG H 83 THR H 87 5 5 HELIX 13 13 SER H 163 ALA H 165 5 3 HELIX 14 14 SER H 196 LEU H 198 5 3 HELIX 15 15 LYS H 213 ASN H 216 5 4 HELIX 16 16 GLU L 80 PHE L 84 5 5 HELIX 17 17 SER L 122 LYS L 127 1 6 HELIX 18 18 LYS L 184 GLU L 188 1 5 SHEET 1 A 7 THR X 39 HIS X 41 0 SHEET 2 A 7 ILE X 68 VAL X 71 1 O VAL X 70 N THR X 39 SHEET 3 A 7 TYR X 103 VAL X 106 1 O ILE X 105 N LEU X 69 SHEET 4 A 7 ARG X 140 ASP X 144 1 O TYR X 142 N VAL X 106 SHEET 5 A 7 GLY X 171 THR X 174 1 O GLY X 171 N PHE X 143 SHEET 6 A 7 ARG X 202 ASP X 206 1 O ASP X 206 N THR X 174 SHEET 7 A 7 ILE X 240 LEU X 244 1 O LEU X 244 N ILE X 205 SHEET 1 B 4 GLN H 3 GLN H 6 0 SHEET 2 B 4 VAL H 18 SER H 25 -1 O GLN H 23 N VAL H 5 SHEET 3 B 4 THR H 77 LEU H 82 -1 O MET H 80 N VAL H 20 SHEET 4 B 4 VAL H 67 ASP H 72 -1 N ASP H 72 O THR H 77 SHEET 1 C 6 GLU H 10 LYS H 12 0 SHEET 2 C 6 THR H 107 VAL H 111 1 O ILE H 110 N LYS H 12 SHEET 3 C 6 ALA H 88 ARG H 94 -1 N TYR H 90 O THR H 107 SHEET 4 C 6 ILE H 34 GLN H 39 -1 N VAL H 37 O TYR H 91 SHEET 5 C 6 PHE H 45 ILE H 51 -1 O MET H 48 N TRP H 36 SHEET 6 C 6 LYS H 57 PHE H 59 -1 O GLU H 58 N TRP H 50 SHEET 1 D 4 GLU H 10 LYS H 12 0 SHEET 2 D 4 THR H 107 VAL H 111 1 O ILE H 110 N LYS H 12 SHEET 3 D 4 ALA H 88 ARG H 94 -1 N TYR H 90 O THR H 107 SHEET 4 D 4 VAL H 102 TRP H 103 -1 O VAL H 102 N ARG H 94 SHEET 1 E 4 SER H 120 LEU H 124 0 SHEET 2 E 4 THR H 137 TYR H 147 -1 O LEU H 143 N PHE H 122 SHEET 3 E 4 TYR H 185 PRO H 194 -1 O TYR H 185 N TYR H 147 SHEET 4 E 4 VAL H 171 THR H 173 -1 N HIS H 172 O VAL H 190 SHEET 1 F 4 SER H 120 LEU H 124 0 SHEET 2 F 4 THR H 137 TYR H 147 -1 O LEU H 143 N PHE H 122 SHEET 3 F 4 TYR H 185 PRO H 194 -1 O TYR H 185 N TYR H 147 SHEET 4 F 4 VAL H 177 LEU H 178 -1 N VAL H 177 O SER H 186 SHEET 1 G 3 THR H 153 TRP H 157 0 SHEET 2 G 3 ILE H 207 HIS H 212 -1 O ASN H 209 N SER H 156 SHEET 3 G 3 THR H 217 LYS H 222 -1 O VAL H 219 N VAL H 210 SHEET 1 H 3 LEU L 4 SER L 7 0 SHEET 2 H 3 ALA L 19 ILE L 29 -1 O ARG L 24 N THR L 5 SHEET 3 H 3 PHE L 63 ILE L 76 -1 O LEU L 74 N PHE L 21 SHEET 1 I 6 THR L 10 LEU L 13 0 SHEET 2 I 6 THR L 103 ARG L 107 1 O LYS L 104 N LEU L 11 SHEET 3 I 6 ALA L 85 VAL L 91 -1 N ALA L 85 O LEU L 105 SHEET 4 I 6 VAL L 34 HIS L 39 -1 N HIS L 39 O LEU L 86 SHEET 5 I 6 ARG L 46 HIS L 50 -1 O ARG L 46 N GLN L 38 SHEET 6 I 6 ASN L 54 ARG L 55 -1 O ASN L 54 N HIS L 50 SHEET 1 J 4 THR L 10 LEU L 13 0 SHEET 2 J 4 THR L 103 ARG L 107 1 O LYS L 104 N LEU L 11 SHEET 3 J 4 ALA L 85 VAL L 91 -1 N ALA L 85 O LEU L 105 SHEET 4 J 4 THR L 98 PHE L 99 -1 O THR L 98 N VAL L 91 SHEET 1 K 4 SER L 115 PHE L 119 0 SHEET 2 K 4 THR L 130 PHE L 140 -1 O ASN L 138 N SER L 115 SHEET 3 K 4 TYR L 174 SER L 183 -1 O TYR L 174 N PHE L 140 SHEET 4 K 4 SER L 160 VAL L 164 -1 N GLN L 161 O THR L 179 SHEET 1 L 4 ALA L 154 LEU L 155 0 SHEET 2 L 4 LYS L 146 VAL L 151 -1 N VAL L 151 O ALA L 154 SHEET 3 L 4 VAL L 192 THR L 198 -1 O GLU L 196 N GLN L 148 SHEET 4 L 4 VAL L 206 ASN L 211 -1 O VAL L 206 N VAL L 197 SSBOND 1 CYS X 220 CYS X 255 1555 1555 2.05 SSBOND 2 CYS H 22 CYS H 92 1555 1555 2.07 SSBOND 3 CYS H 142 CYS H 208 1555 1555 2.05 SSBOND 4 CYS L 23 CYS L 89 1555 1555 2.09 SSBOND 5 CYS L 135 CYS L 195 1555 1555 2.05 CISPEP 1 TYR X 107 PRO X 108 0 -4.79 CISPEP 2 PHE H 148 PRO H 149 0 -8.37 CISPEP 3 GLU H 150 PRO H 151 0 -1.36 CISPEP 4 SER L 7 PRO L 8 0 -6.99 CISPEP 5 TYR L 141 PRO L 142 0 2.86 SITE 1 AC1 8 GLN L 38 ILE L 59 SER L 60 ARG L 62 SITE 2 AC1 8 PHE L 63 GLU L 82 ASP L 83 HOH L 265 SITE 1 AC2 6 TYR X 110 ASP X 144 GLY X 146 MET X 156 SITE 2 AC2 6 HOH X 318 HOH X 356 SITE 1 AC3 12 PHE H 174 PRO H 175 VAL H 177 SER H 186 SITE 2 AC3 12 LEU H 187 SER H 188 GLN L 161 GLU L 162 SITE 3 AC3 12 SER L 177 SER L 178 THR L 179 HOH L 297 SITE 1 AC4 7 LYS X 247 LEU X 248 GLU X 251 GLY X 260 SITE 2 AC4 7 HOH X 313 HOH X 379 HOH X 403 CRYST1 90.453 93.097 94.373 90.00 90.00 90.00 P 21 21 21 4 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 0.011055 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010741 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010596 0.00000