HEADER IMMUNE SYSTEM 29-SEP-98 1BWW TITLE BENCE-JONES IMMUNOGLOBULIN REI VARIABLE PORTION, T39K MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (IG KAPPA CHAIN V-I REGION REI); COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: IMMUNOGLOBULIN KAPPA LIGHT CHAIN; COMPND 5 ENGINEERED: YES; COMPND 6 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; SOURCE 7 EXPRESSION_SYSTEM_CELLULAR_LOCATION: PERIPLASM KEYWDS REIV, STABILIZED IMMUNOGLOBULIN FRAGMENT, BENCE-JONES PROTEIN, IMMUNE KEYWDS 2 SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR I.USON,E.POHL,T.R.SCHNEIDER,Z.DAUTER,A.SCHMIDT,H.J.FRITZ, AUTHOR 2 G.M.SHELDRICK REVDAT 7 30-OCT-24 1BWW 1 REMARK REVDAT 6 09-AUG-23 1BWW 1 REMARK REVDAT 5 03-NOV-21 1BWW 1 REMARK SEQADV REVDAT 4 24-FEB-09 1BWW 1 VERSN REVDAT 3 27-JAN-04 1BWW 1 JRNL REMARK REVDAT 2 29-DEC-99 1BWW 4 HEADER COMPND REMARK JRNL REVDAT 2 2 4 ATOM SOURCE SEQRES REVDAT 1 07-OCT-98 1BWW 0 JRNL AUTH I.USON,E.POHL,T.R.SCHNEIDER,Z.DAUTER,A.SCHMIDT,H.J.FRITZ, JRNL AUTH 2 G.M.SHELDRICK JRNL TITL 1.7 A STRUCTURE OF THE STABILIZED REIV MUTANT T39K. JRNL TITL 2 APPLICATION OF LOCAL NCS RESTRAINTS. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 55 1158 1999 JRNL REFN ISSN 0907-4449 JRNL PMID 10329778 JRNL DOI 10.1107/S0907444999003972 REMARK 2 REMARK 2 RESOLUTION. 1.70 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.182 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.181 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1113 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 22266 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.158 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.156 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 878 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 17229 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1686 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 92 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1778.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 1640.0 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 4 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 7201 REMARK 3 NUMBER OF RESTRAINTS : 9275 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 ANGLE DISTANCES (A) : 0.023 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.025 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.026 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.106 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.098 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.013 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.061 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, REMARK 3 J.APPL.CRYST.28 (1995)53-56 B23 (A**2) : ESTIMATED OVERALL REMARK 3 COORDINATE ERROR. REMARK 3 REMARK 3 THE STRUCTURE WAS REFINED USING LOCAL NCS RESTRAINTS REMARK 4 REMARK 4 1BWW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB. REMARK 100 THE DEPOSITION ID IS D_1000008245. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAR-95 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : BW7B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.87 REMARK 200 MONOCHROMATOR : GE SINGLE CRYSTAL REMARK 200 OPTICS : BENT CRYSTAL 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 : 22266 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 45.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 200 DATA REDUNDANCY : 1.800 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL 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) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.1 REMARK 200 DATA REDUNDANCY IN SHELL : 0.95 REMARK 200 R MERGE FOR SHELL (I) : 0.31800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: REI WILDTYPE 1REI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 8000, 100 MM HEPES PH7 10 REMARK 280 MG/ML PROTEIN IN 50 MM PHOSPHATE PH7, PH 7.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1410 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 CYS A 25 CA - CB - SG ANGL. DEV. = 14.4 DEGREES REMARK 500 ARG B 63 NE - CZ - NH1 ANGL. DEV. = 3.0 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 ILE A 32 -73.63 66.21 REMARK 500 LYS A 33 11.12 -153.35 REMARK 500 ALA A 53 -39.85 69.95 REMARK 500 ILE B 32 -77.41 65.28 REMARK 500 LYS B 33 15.23 -152.17 REMARK 500 ALA B 53 -40.83 70.62 REMARK 500 ALA B 86 -178.65 -173.48 REMARK 500 REMARK 500 REMARK: NULL DBREF 1BWW A 3 109 UNP P01607 KV1O_HUMAN 1 107 DBREF 1BWW B 3 109 UNP P01607 KV1O_HUMAN 1 107 SEQADV 1BWW THR A 1 UNP P01607 CONFLICT SEQADV 1BWW PRO A 2 UNP P01607 CONFLICT SEQADV 1BWW LYS A 41 UNP P01607 THR 39 ENGINEERED MUTATION SEQADV 1BWW THR B 1 UNP P01607 CONFLICT SEQADV 1BWW PRO B 2 UNP P01607 CONFLICT SEQADV 1BWW LYS B 41 UNP P01607 THR 39 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 CYS GLN SEQRES 3 A 109 ALA SER GLN ASP ILE ILE LYS TYR LEU ASN TRP TYR GLN SEQRES 4 A 109 GLN LYS 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 SEQRES 1 B 109 THR PRO ASP ILE GLN MET THR GLN SER PRO SER SER LEU SEQRES 2 B 109 SER ALA SER VAL GLY ASP ARG VAL THR ILE THR CYS GLN SEQRES 3 B 109 ALA SER GLN ASP ILE ILE LYS TYR LEU ASN TRP TYR GLN SEQRES 4 B 109 GLN LYS PRO GLY LYS ALA PRO LYS LEU LEU ILE TYR GLU SEQRES 5 B 109 ALA SER ASN LEU GLN ALA GLY VAL PRO SER ARG PHE SER SEQRES 6 B 109 GLY SER GLY SER GLY THR ASP TYR THR PHE THR ILE SER SEQRES 7 B 109 SER LEU GLN PRO GLU ASP ILE ALA THR TYR TYR CYS GLN SEQRES 8 B 109 GLN TYR GLN SER LEU PRO TYR THR PHE GLY GLN GLY THR SEQRES 9 B 109 LYS LEU GLN ILE THR FORMUL 3 HOH *92(H2 O) HELIX 1 1 PRO A 82 ASP A 84 5 3 HELIX 2 2 PRO B 82 ASP B 84 5 3 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 5 SER A 12 ALA A 15 0 SHEET 2 B 5 THR A 104 ILE A 108 1 N LYS A 105 O LEU A 13 SHEET 3 B 5 ALA A 86 GLN A 92 -1 N TYR A 88 O THR A 104 SHEET 4 B 5 LEU A 35 GLN A 40 -1 N GLN A 40 O THR A 87 SHEET 5 B 5 LYS A 47 ILE A 50 -1 N ILE A 50 O TRP A 37 SHEET 1 C 4 MET B 6 SER B 9 0 SHEET 2 C 4 VAL B 21 ALA B 27 -1 N GLN B 26 O THR B 7 SHEET 3 C 4 ASP B 72 ILE B 77 -1 N ILE B 77 O VAL B 21 SHEET 4 C 4 PHE B 64 SER B 69 -1 N SER B 69 O ASP B 72 SHEET 1 D 2 SER B 12 ALA B 15 0 SHEET 2 D 2 LYS B 105 ILE B 108 1 N LYS B 105 O LEU B 13 SHEET 1 E 3 THR B 87 GLN B 92 0 SHEET 2 E 3 LEU B 35 GLN B 40 -1 N GLN B 40 O THR B 87 SHEET 3 E 3 LYS B 47 ILE B 50 -1 N ILE B 50 O TRP B 37 SSBOND 1 CYS A 25 CYS A 90 1555 1555 1.98 SSBOND 2 CYS B 25 CYS B 90 1555 1555 1.98 CISPEP 1 SER A 9 PRO A 10 0 -3.54 CISPEP 2 LEU A 96 PRO A 97 0 -1.04 CISPEP 3 SER B 9 PRO B 10 0 -3.60 CISPEP 4 LEU B 96 PRO B 97 0 -0.74 CRYST1 35.400 40.100 43.100 66.90 85.40 73.80 P 1 2 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 0.028248 -0.008207 0.000975 0.00000 SCALE2 0.000000 0.025969 -0.010883 0.00000 SCALE3 0.000000 0.000000 0.025238 0.00000 MTRIX1 1 -0.999770 -0.017890 0.012120 -2.00585 1 MTRIX2 1 -0.021190 0.701760 -0.712100 0.55889 1 MTRIX3 1 0.004240 -0.712190 -0.701980 1.45528 1