HEADER IMMUNE SYSTEM 06-DEC-06 2O5Y TITLE CRYSTAL STRUCTURE OF THE 1E9 LEUH47TRP/ARGH100TRP FAB PROGESTERONE TITLE 2 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHIMERIC ANTIBODY FAB 1E9-DB3; COMPND 3 CHAIN: L; COMPND 4 FRAGMENT: LIGHT CHAIN; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: CHIMERIC ANTIBODY FAB 1E9-DB3; COMPND 9 CHAIN: H; COMPND 10 FRAGMENT: HEAVY CHAIN; COMPND 11 ENGINEERED: YES; COMPND 12 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS, HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE, HUMAN; SOURCE 4 ORGANISM_TAXID: 10090,9606; SOURCE 5 STRAIN: ,; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: TOPP2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: P4XH-1E9; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: MUS MUSCULUS, HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HOUSE MOUSE, HUMAN; SOURCE 14 ORGANISM_TAXID: 10090,9606; SOURCE 15 STRAIN: ,; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: TOPP2; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: P4XH-1E9 KEYWDS IMMUNOGLOBULIN, CHIMERIC FAB, ANTIBODY ENGINEERING, EVOLUTION OF KEYWDS 2 LIGAND RECOGNITION, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR P.VERDINO,I.A.WILSON REVDAT 5 27-DEC-23 2O5Y 1 REMARK REVDAT 4 13-JUL-11 2O5Y 1 VERSN REVDAT 3 24-FEB-09 2O5Y 1 VERSN REVDAT 2 30-SEP-08 2O5Y 1 JRNL REVDAT 1 18-DEC-07 2O5Y 0 JRNL AUTH P.VERDINO,C.ALDAG,D.HILVERT,I.A.WILSON JRNL TITL CLOSELY RELATED ANTIBODY RECEPTORS EXPLOIT FUNDAMENTALLY JRNL TITL 2 DIFFERENT STRATEGIES FOR STEROID RECOGNITION. JRNL REF PROC.NATL.ACAD.SCI.USA V. 105 11725 2008 JRNL REFN ISSN 0027-8424 JRNL PMID 18689687 JRNL DOI 10.1073/PNAS.0801783105 REMARK 2 REMARK 2 RESOLUTION. 2.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 19177 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) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1034 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) : 2.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.92 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1426 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.30 REMARK 3 BIN R VALUE (WORKING SET) : 0.2760 REMARK 3 BIN FREE R VALUE SET COUNT : 73 REMARK 3 BIN FREE R VALUE : 0.3510 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3349 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 88 REMARK 3 SOLVENT ATOMS : 65 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 52.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.13 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.23000 REMARK 3 B22 (A**2) : 3.23000 REMARK 3 B33 (A**2) : -4.85000 REMARK 3 B12 (A**2) : 1.62000 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): 0.443 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.295 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.224 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 24.013 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.940 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.890 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3522 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4805 ; 1.649 ; 1.976 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 435 ; 7.174 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 135 ;34.901 ;24.593 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 554 ;20.020 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;19.889 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 527 ; 0.102 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2604 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1421 ; 0.222 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2384 ; 0.318 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 129 ; 0.145 ; 0.200 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): 34 ; 0.180 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 6 ; 0.189 ; 0.200 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): 2203 ; 0.555 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3524 ; 1.056 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1488 ; 1.673 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1281 ; 2.763 ; 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 : NULL 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 : 1.20 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 2O5Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-DEC-06. REMARK 100 THE DEPOSITION ID IS D_1000040728. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-NOV-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99996 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20438 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.850 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.11100 REMARK 200 R SYM (I) : 11.1000 REMARK 200 FOR THE DATA SET : 9.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 0.38200 REMARK 200 R SYM FOR SHELL (I) : 38.2000 REMARK 200 FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: RIGID BODY REFINEMENT REMARK 200 SOFTWARE USED: REFMAC 5.2.0019 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 73.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5 M AMMONIUM SULFATE, 0.15 M SODIUM REMARK 280 CITRATE, 0.01% PEG 20000, PH 7.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 295.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 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 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 30.60533 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 61.21067 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 61.21067 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 30.60533 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 5310 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20600 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -148.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, H 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8490 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 43700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -310.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: H 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 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -30.60533 REMARK 350 APPLY THE FOLLOWING TO CHAINS: L REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 128.35400 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 -30.60533 REMARK 350 BIOMT1 4 -0.500000 0.866025 0.000000 128.35400 REMARK 350 BIOMT2 4 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 14220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 37970 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -334.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, H 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 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -30.60533 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 CYS L 214 REMARK 465 LEU H 228 REMARK 465 SER H 229 REMARK 465 CYS H 230 REMARK 465 ASP H 232 REMARK 465 LYS H 235 REMARK 465 THR H 236 REMARK 465 HIS H 237 REMARK 465 THR H 238 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 CYS H 142 CB CYS H 142 SG -0.104 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 PRO H 227 C - N - CA ANGL. DEV. = 9.3 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 TYR L 32 65.14 -103.13 REMARK 500 PRO L 40 129.18 -38.52 REMARK 500 PRO L 44 156.23 -49.01 REMARK 500 LEU L 47 -66.64 -100.18 REMARK 500 VAL L 51 -53.88 75.22 REMARK 500 SER L 65 -169.16 -164.92 REMARK 500 ARG L 77 60.51 34.73 REMARK 500 LEU L 83 125.94 -34.30 REMARK 500 VAL L 110 140.90 -36.92 REMARK 500 LYS L 190 -36.94 -130.48 REMARK 500 MET H 28 103.44 -54.25 REMARK 500 ALA H 88 174.44 178.37 REMARK 500 ASP H 146 61.95 62.49 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 SO4 L 215 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 L 216 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 H 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 H 239 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 H 240 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 H 241 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 H 242 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 H 243 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 H 244 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 H 245 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 H 246 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 H 247 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 H 248 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE STR H 249 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2O5X RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF 1E9-DB3, A HYBRID FAB BETWEEN A DIELS-ALDERASE REMARK 900 AND A STEROID-BINDING ANTIBODY REMARK 900 RELATED ID: 2O5Z RELATED DB: PDB REMARK 900 1E9-DB3 HYBRID FAB 5-BETA-ANDROSTANE-1,3-DIONE COMPLEX REMARK 999 REMARK 999 SEQUENCE REMARK 999 THERE IS NO AMINOACID SEQUENCE DATABASE REFERENCE REMARK 999 AVAILABLE FOR THE PROTEIN. THE PROTEIN WAS DESIGNED USING REMARK 999 VARIABLE DOMAINS FROM MOUSE AND THE CONSTANT DOMAINS FROM REMARK 999 HUMANS DBREF 2O5Y L 1 214 PDB 2O5Y 2O5Y 1 214 DBREF 2O5Y H 1 238 PDB 2O5Y 2O5Y 1 238 SEQRES 1 L 219 GLU LEU VAL MET THR GLN THR PRO LEU SER LEU PRO VAL SEQRES 2 L 219 SER LEU GLY ASP GLN ALA SER ILE SER CYS ARG SER SER SEQRES 3 L 219 GLN SER LEU VAL HIS SER ASN GLY ASN THR TYR LEU HIS SEQRES 4 L 219 TRP TYR LEU GLN LYS PRO GLY GLN SER PRO LYS PHE LEU SEQRES 5 L 219 ILE TYR LYS VAL SER ASN ARG PHE SER GLY VAL PRO ASP SEQRES 6 L 219 ARG PHE SER GLY SER GLY SER GLY THR ASP PHE ILE LEU SEQRES 7 L 219 LYS ILE SER ARG VAL GLU ALA GLU ASP LEU GLY VAL TYR SEQRES 8 L 219 PHE CYS PHE GLN SER THR HIS PHE PHE PRO THR PHE GLY SEQRES 9 L 219 GLY GLY THR LYS LEU GLU ILE LYS ARG THR VAL ALA ALA SEQRES 10 L 219 PRO SER VAL PHE ILE PHE PRO PRO SER ASP GLU GLN LEU SEQRES 11 L 219 LYS SER GLY THR ALA SER VAL VAL CYS LEU LEU ASN ASN SEQRES 12 L 219 PHE TYR PRO ARG GLU ALA LYS VAL GLN TRP LYS VAL ASP SEQRES 13 L 219 ASN ALA LEU GLN SER GLY ASN SER GLN GLU SER VAL THR SEQRES 14 L 219 GLU GLN ASP SER LYS ASP SER THR TYR SER LEU SER SER SEQRES 15 L 219 THR LEU THR LEU SER LYS ALA ASP TYR GLU LYS HIS LYS SEQRES 16 L 219 VAL TYR ALA CYS GLU VAL THR HIS GLN GLY LEU SER SER SEQRES 17 L 219 PRO VAL THR LYS SER PHE ASN ARG GLY GLU CYS SEQRES 1 H 227 GLN VAL GLN LEU VAL GLN SER GLY PRO GLU LEU LYS LYS SEQRES 2 H 227 PRO GLY GLU THR VAL LYS ILE SER CYS LYS ALA SER GLY SEQRES 3 H 227 TYR MET PHE THR ASN TYR GLY MET ASN TRP VAL LYS GLN SEQRES 4 H 227 ALA PRO GLY LYS ALA LEU LYS TRP MET GLY TRP ILE ASN SEQRES 5 H 227 PRO TYR THR GLY GLU SER THR PHE ALA ASP ASP PHE LYS SEQRES 6 H 227 GLY ARG PHE ALA PHE PHE LEU GLU THR SER ALA THR THR SEQRES 7 H 227 ALA TYR LEU GLN ILE ASN ASN LEU LYS ASN GLU ASP THR SEQRES 8 H 227 ALA THR TYR PHE CYS ALA ARG GLY THR THR ILE VAL TRP SEQRES 9 H 227 ALA MET ASP TYR TRP GLY GLN GLY THR SER VAL THR VAL SEQRES 10 H 227 SER SER ALA SER THR LYS GLY PRO SER VAL PHE PRO LEU SEQRES 11 H 227 ALA PRO SER SER LYS SER THR SER GLY GLY THR ALA ALA SEQRES 12 H 227 LEU GLY CYS LEU VAL LYS ASP TYR PHE PRO GLU PRO VAL SEQRES 13 H 227 THR VAL SER TRP ASN SER GLY ALA LEU THR SER GLY VAL SEQRES 14 H 227 HIS THR PHE PRO ALA VAL LEU GLN SER SER GLY LEU TYR SEQRES 15 H 227 SER LEU SER SER VAL VAL THR VAL PRO SER SER SER LEU SEQRES 16 H 227 GLY THR GLN THR TYR ILE CYS ASN VAL ASN HIS LYS PRO SEQRES 17 H 227 SER ASN THR LYS VAL ASP LYS LYS VAL GLU PRO LEU SER SEQRES 18 H 227 CYS ASP LYS THR HIS THR HET SO4 L 215 10 HET SO4 L 216 5 HET SO4 H 201 5 HET SO4 H 239 5 HET SO4 H 240 5 HET SO4 H 241 5 HET SO4 H 242 5 HET SO4 H 243 5 HET SO4 H 244 5 HET SO4 H 245 5 HET SO4 H 246 5 HET SO4 H 247 5 HET SO4 H 248 5 HET STR H 249 23 HETNAM SO4 SULFATE ION HETNAM STR PROGESTERONE FORMUL 3 SO4 13(O4 S 2-) FORMUL 16 STR C21 H30 O2 FORMUL 17 HOH *65(H2 O) HELIX 1 1 GLU L 79 LEU L 83 5 5 HELIX 2 2 SER L 121 GLY L 128 1 8 HELIX 3 3 LYS L 183 LYS L 188 1 6 HELIX 4 4 MET H 28 TYR H 32 5 5 HELIX 5 5 ASP H 61 LYS H 64 5 4 HELIX 6 6 THR H 73 ALA H 75 5 3 HELIX 7 7 LYS H 83 THR H 87 5 5 HELIX 8 8 SER H 196 LEU H 200 5 3 SHEET 1 A 4 MET L 4 THR L 7 0 SHEET 2 A 4 ALA L 19 SER L 25 -1 O SER L 22 N THR L 7 SHEET 3 A 4 ASP L 70 ILE L 75 -1 O LEU L 73 N ILE L 21 SHEET 4 A 4 PHE L 62 SER L 67 -1 N SER L 63 O LYS L 74 SHEET 1 B 6 SER L 10 SER L 14 0 SHEET 2 B 6 THR L 102 LYS L 107 1 O GLU L 105 N VAL L 13 SHEET 3 B 6 GLY L 84 GLN L 90 -1 N TYR L 86 O THR L 102 SHEET 4 B 6 LEU L 33 GLN L 38 -1 N HIS L 34 O PHE L 89 SHEET 5 B 6 LYS L 45 TYR L 49 -1 O LEU L 47 N TRP L 35 SHEET 6 B 6 ASN L 53 ARG L 54 -1 O ASN L 53 N TYR L 49 SHEET 1 C 4 SER L 10 SER L 14 0 SHEET 2 C 4 THR L 102 LYS L 107 1 O GLU L 105 N VAL L 13 SHEET 3 C 4 GLY L 84 GLN L 90 -1 N TYR L 86 O THR L 102 SHEET 4 C 4 THR L 97 PHE L 98 -1 O THR L 97 N GLN L 90 SHEET 1 D 4 SER L 114 PHE L 118 0 SHEET 2 D 4 THR L 129 PHE L 139 -1 O ASN L 137 N SER L 114 SHEET 3 D 4 TYR L 173 SER L 182 -1 O TYR L 173 N PHE L 139 SHEET 4 D 4 SER L 159 VAL L 163 -1 N SER L 162 O SER L 176 SHEET 1 E 4 ALA L 153 LEU L 154 0 SHEET 2 E 4 LYS L 145 VAL L 150 -1 N VAL L 150 O ALA L 153 SHEET 3 E 4 VAL L 191 THR L 197 -1 O GLU L 195 N GLN L 147 SHEET 4 E 4 VAL L 205 ASN L 210 -1 O VAL L 205 N VAL L 196 SHEET 1 F 4 GLN H 3 GLN H 6 0 SHEET 2 F 4 VAL H 18 SER H 25 -1 O LYS H 23 N VAL H 5 SHEET 3 F 4 THR H 77 ILE H 82 -1 O LEU H 80 N ILE H 20 SHEET 4 F 4 PHE H 67 GLU H 72 -1 N ALA H 68 O GLN H 81 SHEET 1 G 6 GLU H 10 LYS H 12 0 SHEET 2 G 6 THR H 107 VAL H 111 1 O THR H 110 N GLU H 10 SHEET 3 G 6 ALA H 88 THR H 96 -1 N TYR H 90 O THR H 107 SHEET 4 G 6 GLY H 33 GLN H 39 -1 N VAL H 37 O PHE H 91 SHEET 5 G 6 LYS H 46 ILE H 51 -1 O ILE H 51 N MET H 34 SHEET 6 G 6 SER H 57 PHE H 59 -1 O THR H 58 N TRP H 50 SHEET 1 H 4 GLU H 10 LYS H 12 0 SHEET 2 H 4 THR H 107 VAL H 111 1 O THR H 110 N GLU H 10 SHEET 3 H 4 ALA H 88 THR H 96 -1 N TYR H 90 O THR H 107 SHEET 4 H 4 ALA H 100A TRP H 103 -1 O TYR H 102 N ARG H 94 SHEET 1 I 4 SER H 120 LEU H 124 0 SHEET 2 I 4 THR H 137 TYR H 147 -1 O GLY H 141 N LEU H 124 SHEET 3 I 4 TYR H 185 PRO H 194 -1 O VAL H 191 N LEU H 140 SHEET 4 I 4 VAL H 171 THR H 173 -1 N HIS H 172 O VAL H 190 SHEET 1 J 4 SER H 120 LEU H 124 0 SHEET 2 J 4 THR H 137 TYR H 147 -1 O GLY H 141 N LEU H 124 SHEET 3 J 4 TYR H 185 PRO H 194 -1 O VAL H 191 N LEU H 140 SHEET 4 J 4 VAL H 177 LEU H 178 -1 N VAL H 177 O SER H 186 SHEET 1 K 3 THR H 153 TRP H 157 0 SHEET 2 K 3 TYR H 206 HIS H 212 -1 O ASN H 211 N THR H 153 SHEET 3 K 3 THR H 217 VAL H 223 -1 O VAL H 219 N VAL H 210 SSBOND 1 CYS L 23 CYS L 88 1555 1555 2.13 SSBOND 2 CYS L 134 CYS L 194 1555 1555 2.05 SSBOND 3 CYS H 22 CYS H 92 1555 1555 2.06 SSBOND 4 CYS H 142 CYS H 208 1555 1555 2.07 CISPEP 1 THR L 7 PRO L 8 0 -11.78 CISPEP 2 PHE L 94 PHE L 95 0 6.19 CISPEP 3 TYR L 140 PRO L 141 0 -3.29 CISPEP 4 PHE H 148 PRO H 149 0 -3.29 CISPEP 5 GLU H 150 PRO H 151 0 -0.67 SITE 1 AC1 3 GLU H 56 SER H 57 ARG L 211 SITE 1 AC2 4 PRO L 8 LEU L 9 SER L 10 SER L 156 SITE 1 AC3 3 SER H 25 GLY H 26 TYR H 27 SITE 1 AC4 5 ASN H 84 SER H 112 SER H 113 ARG L 108 SITE 2 AC4 5 ALA L 111 SITE 1 AC5 2 ARG H 66 LYS H 83 SITE 1 AC6 3 GLU H 72 THR H 73 SER H 74 SITE 1 AC7 2 SER H 7 GLY H 8 SITE 1 AC8 2 LYS H 221 LYS H 222 SITE 1 AC9 2 LYS H 117 GLY H 118 SITE 1 BC1 4 LYS H 13 SER H 115 HOH H 261 SER L 202 SITE 1 BC2 4 TYR H 27 MET H 28 TYR H 32 HOH H 255 SITE 1 BC3 4 SER H 180 LYS L 107 GLY L 157 GLN L 160 SITE 1 BC4 3 LYS H 43 ALA H 44 LYS H 46 SITE 1 BC5 5 ASN H 35 TRP H 50 ALA H 100A MET H 100B SITE 2 BC5 5 ASN L 28 CRYST1 128.354 128.354 91.816 90.00 90.00 120.00 P 31 2 1 6 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 0.007791 0.004498 0.000000 0.00000 SCALE2 0.000000 0.008996 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010891 0.00000