HEADER IMMUNOGLOBULIN 08-AUG-97 1AR2 TITLE DISULFIDE-FREE IMMUNOGLOBULIN FRAGMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: REI; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: VARIABLE REGION, LIGHT CHAIN; COMPND 5 SYNONYM: IG KAPPA CHAIN V-I REGION; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DISULFIDE-FREE, IMMUNOGLOBULIN FRAGMENT, BENCE-JONES, IMMUNOGLOBULIN EXPDTA X-RAY DIFFRACTION AUTHOR I.USON,M.T.BES,G.M.SHELDRICK,T.R.SCHNEIDER,T.HARTSCH,H.-J.FRITZ REVDAT 5 22-MAY-24 1AR2 1 REMARK REVDAT 4 02-AUG-23 1AR2 1 REMARK REVDAT 3 03-NOV-21 1AR2 1 REMARK SEQADV REVDAT 2 24-FEB-09 1AR2 1 VERSN REVDAT 1 12-NOV-97 1AR2 0 JRNL AUTH I.USON,M.T.BES,G.M.SHELDRICK,T.R.SCHNEIDER,T.HARTSCH, JRNL AUTH 2 H.J.FRITZ JRNL TITL X-RAY CRYSTALLOGRAPHY REVEALS STRINGENT CONSERVATION OF JRNL TITL 2 PROTEIN FOLD AFTER REMOVAL OF THE ONLY DISULFIDE BRIDGE FROM JRNL TITL 3 A STABILIZED IMMUNOGLOBULIN VARIABLE DOMAIN. JRNL REF STRUCTURE FOLD.DES. V. 2 357 1997 JRNL REFN ISSN 0969-2126 JRNL PMID 9427009 JRNL DOI 10.1016/S1359-0278(97)00049-7 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 75.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : EVERY 10TH REFLECTION REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.280 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.254 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.415 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 340 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 3528 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.228 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.200 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.356 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 267 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 2639 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 840 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 17 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 857.50 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 819.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 3434 REMARK 3 NUMBER OF RESTRAINTS : 4775 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.004 REMARK 3 ANGLE DISTANCES (A) : 0.017 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.041 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.053 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.061 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.010 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.016 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: SIMULATED ANNEALING WITH X-PLOR, FINAL REMARK 3 REFINEMENT WITH SHELXL-97 REMARK 4 REMARK 4 1AR2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000171152. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-AUG-96 REMARK 200 TEMPERATURE (KELVIN) : 277 REMARK 200 PH : 4.6-7.0 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : BW7A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.901 REMARK 200 MONOCHROMATOR : GE(111) REMARK 200 OPTICS : BENT CRYSTAL MONOCHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3549 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 75.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 10.70 REMARK 200 R MERGE (I) : 0.10400 REMARK 200 R SYM (I) : 0.08800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.37600 REMARK 200 R SYM FOR SHELL (I) : 0.43000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: SHELXL-97 REMARK 200 STARTING MODEL: PDB ENTRY 1REI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: VAPOUR DIFFUSION AL 4 C FROM A PROTEIN REMARK 280 SOLUTION CONTAINING 8 MG/ML IN 50 MM POTASSIUM PHOSPHATE BUFFER REMARK 280 AL PH 7, USING 2 M AMMONIUM SULFATE IN 100 MM SODIUM ACETATE REMARK 280 BUFFER, PH 4.6, VAPOR DIFFUSION, TEMPERATURE 277K 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 52.73333 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 105.46667 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 79.10000 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 131.83333 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 26.36667 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 52.73333 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 105.46667 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 131.83333 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 79.10000 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 26.36667 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: DIMERIC 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 BIOMT1 2 -1.000000 0.000000 0.000000 52.80000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 79.10000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 126 LIES ON A SPECIAL POSITION. 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 ARG A 20 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 63 NE - CZ - NH1 ANGL. DEV. = 3.1 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 SER A 12 139.62 177.30 REMARK 500 ILE A 32 -156.06 46.87 REMARK 500 ALA A 53 -24.50 68.24 REMARK 500 SER A 54 -14.91 -143.39 REMARK 500 GLN A 57 -158.45 -73.55 REMARK 500 LEU A 80 103.39 85.79 REMARK 500 REMARK 500 REMARK: NULL DBREF 1AR2 A 3 109 UNP P01607 KV1O_HUMAN 1 107 SEQADV 1AR2 VAL A 25 UNP P01607 CYS 23 ENGINEERED MUTATION SEQADV 1AR2 HIS A 34 UNP P01607 TYR 32 ENGINEERED MUTATION SEQRES 1 A 109 THR PRO ASP ILE GLN MET THR GLN SER PRO SER SER LEU SEQRES 2 A 109 SER ALA SER VAL GLY ASP ARG VAL THR ILE THR VAL GLN SEQRES 3 A 109 ALA SER GLN ASP ILE ILE LYS HIS LEU ASN TRP TYR GLN SEQRES 4 A 109 GLN THR PRO GLY LYS ALA PRO LYS LEU LEU ILE TYR GLU SEQRES 5 A 109 ALA SER ASN LEU GLN ALA GLY VAL PRO SER ARG PHE SER SEQRES 6 A 109 GLY SER GLY SER GLY THR ASP TYR THR PHE THR ILE SER SEQRES 7 A 109 SER LEU GLN PRO GLU ASP ILE ALA THR TYR TYR CYS GLN SEQRES 8 A 109 GLN TYR GLN SER LEU PRO TYR THR PHE GLY GLN GLY THR SEQRES 9 A 109 LYS LEU GLN ILE THR FORMUL 2 HOH *17(H2 O) HELIX 1 1 GLN A 81 ILE A 85 5 5 SHEET 1 A 4 MET A 6 SER A 9 0 SHEET 2 A 4 VAL A 21 ALA A 27 -1 N GLN A 26 O THR A 7 SHEET 3 A 4 ASP A 72 ILE A 77 -1 N ILE A 77 O VAL A 21 SHEET 4 A 4 PHE A 64 SER A 69 -1 N SER A 69 O ASP A 72 SHEET 1 B 3 THR A 87 GLN A 92 0 SHEET 2 B 3 LEU A 35 GLN A 40 -1 N GLN A 40 O THR A 87 SHEET 3 B 3 LYS A 47 ILE A 50 -1 N ILE A 50 O TRP A 37 CISPEP 1 SER A 9 PRO A 10 0 -3.30 CISPEP 2 LEU A 96 PRO A 97 0 -2.41 CRYST1 52.800 52.800 158.200 90.00 90.00 120.00 P 61 2 2 12 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 0.018939 0.010935 0.000000 0.00000 SCALE2 0.000000 0.021869 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006321 0.00000