HEADER IMMUNOGLOBULIN 12-MAY-98 4LVE TITLE LEN K30T MUTANT: A DOMAIN FLIP AS A RESULT OF A SINGLE AMINO ACID TITLE 2 SUBSTITUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: LEN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 OTHER_DETAILS: KAPPA-IV LIGHT CHAIN DIMER 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_STRAIN: JM83 KEYWDS IMMUNOGLOBULIN, KAPPA-IV, LIGHT CHAIN DIMER EXPDTA X-RAY DIFFRACTION AUTHOR M.SCHIFFER,P.R.POKKULURI REVDAT 4 09-AUG-23 4LVE 1 REMARK REVDAT 3 03-NOV-21 4LVE 1 SEQADV REVDAT 2 24-FEB-09 4LVE 1 VERSN REVDAT 1 18-MAY-99 4LVE 0 JRNL AUTH P.R.POKKULURI,D.B.HUANG,R.RAFFEN,X.CAI,G.JOHNSON, JRNL AUTH 2 P.W.STEVENS,F.J.STEVENS,M.SCHIFFER JRNL TITL A DOMAIN FLIP AS A RESULT OF A SINGLE AMINO-ACID JRNL TITL 2 SUBSTITUTION. JRNL REF STRUCTURE V. 6 1067 1998 JRNL REFN ISSN 0969-2126 JRNL PMID 9739086 JRNL DOI 10.1016/S0969-2126(98)00107-5 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.3C REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 944500.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 89.2 REMARK 3 NUMBER OF REFLECTIONS : 9338 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 SET) : 0.190 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 941 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.44 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 81.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1248 REMARK 3 BIN R VALUE (WORKING SET) : 0.2340 REMARK 3 BIN FREE R VALUE : 0.3040 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 152 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.025 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1752 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 201 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -17.79000 REMARK 3 B22 (A**2) : 5.02000 REMARK 3 B33 (A**2) : 12.77000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM SIGMAA (A) : 0.18 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.37 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.33 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.720 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.290 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.030 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.030 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.820 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.44 REMARK 3 BSOL : 55.00 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : CNS_TOPPAR:PROTEIN_REP.PA REMARK 3 PARAMETER FILE 2 : CNS_TOPPAR:WATER_REP.PARA REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : CNS_TOPPAR:PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : CNS_TOPPAR:WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4LVE 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_1000179359. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : FEB-98 REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH2R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16282 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.2 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : 0.05900 REMARK 200 FOR THE DATA SET : 18.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.21900 REMARK 200 R SYM FOR SHELL (I) : 0.21900 REMARK 200 FOR SHELL : 5.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: DIMER GENERATED FROM 3LVE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.5 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 23.10000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 45.70000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.30000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 45.70000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.10000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.30000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 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 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 ARG B 408 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 LYS A 39 CG CD CE NZ REMARK 470 ARG A 108 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 379 CG CD OE1 NE2 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 51 -30.54 74.68 REMARK 500 ALA B 351 -32.12 76.59 REMARK 500 ASP B 360 1.52 -61.92 REMARK 500 ALA B 384 -178.34 -176.65 REMARK 500 REMARK 500 REMARK: NULL DBREF 4LVE A 1 108 UNP P01625 KV4A_HUMAN 1 114 DBREF 4LVE B 301 408 UNP P01625 KV4A_HUMAN 1 114 SEQADV 4LVE THR A 30 UNP P01625 LYS 36 ENGINEERED MUTATION SEQADV 4LVE THR B 330 UNP P01625 LYS 36 ENGINEERED MUTATION SEQRES 1 A 114 ASP ILE VAL MET THR GLN SER PRO ASP SER LEU ALA VAL SEQRES 2 A 114 SER LEU GLY GLU ARG ALA THR ILE ASN CYS LYS SER SER SEQRES 3 A 114 GLN SER VAL LEU TYR SER SER ASN SER THR ASN TYR LEU SEQRES 4 A 114 ALA TRP TYR GLN GLN LYS PRO GLY GLN PRO PRO LYS LEU SEQRES 5 A 114 LEU ILE TYR TRP ALA SER THR ARG GLU SER GLY VAL PRO SEQRES 6 A 114 ASP ARG PHE SER GLY SER GLY SER GLY THR ASP PHE THR SEQRES 7 A 114 LEU THR ILE SER SER LEU GLN ALA GLU ASP VAL ALA VAL SEQRES 8 A 114 TYR TYR CYS GLN GLN TYR TYR SER THR PRO TYR SER PHE SEQRES 9 A 114 GLY GLN GLY THR LYS LEU GLU ILE LYS ARG SEQRES 1 B 114 ASP ILE VAL MET THR GLN SER PRO ASP SER LEU ALA VAL SEQRES 2 B 114 SER LEU GLY GLU ARG ALA THR ILE ASN CYS LYS SER SER SEQRES 3 B 114 GLN SER VAL LEU TYR SER SER ASN SER THR ASN TYR LEU SEQRES 4 B 114 ALA TRP TYR GLN GLN LYS PRO GLY GLN PRO PRO LYS LEU SEQRES 5 B 114 LEU ILE TYR TRP ALA SER THR ARG GLU SER GLY VAL PRO SEQRES 6 B 114 ASP ARG PHE SER GLY SER GLY SER GLY THR ASP PHE THR SEQRES 7 B 114 LEU THR ILE SER SER LEU GLN ALA GLU ASP VAL ALA VAL SEQRES 8 B 114 TYR TYR CYS GLN GLN TYR TYR SER THR PRO TYR SER PHE SEQRES 9 B 114 GLY GLN GLY THR LYS LEU GLU ILE LYS ARG FORMUL 3 HOH *201(H2 O) HELIX 1 1 ALA A 80 ASP A 82 5 3 HELIX 2 2 ALA B 380 ASP B 382 5 3 SHEET 1 A 4 MET A 4 SER A 7 0 SHEET 2 A 4 ALA A 19 SER A 25 -1 N LYS A 24 O THR A 5 SHEET 3 A 4 ASP A 70 ILE A 75 -1 N ILE A 75 O ALA A 19 SHEET 4 A 4 PHE A 62 SER A 67 -1 N SER A 67 O ASP A 70 SHEET 1 B 5 SER A 10 VAL A 13 0 SHEET 2 B 5 THR A 102 ILE A 106 1 N LYS A 103 O LEU A 11 SHEET 3 B 5 ALA A 84 GLN A 90 -1 N TYR A 86 O THR A 102 SHEET 4 B 5 LEU A 33 GLN A 38 -1 N GLN A 38 O VAL A 85 SHEET 5 B 5 LYS A 45 TYR A 49 -1 N ILE A 48 O TRP A 35 SHEET 1 C 4 MET B 304 SER B 307 0 SHEET 2 C 4 ALA B 319 SER B 325 -1 N LYS B 324 O THR B 305 SHEET 3 C 4 ASP B 370 ILE B 375 -1 N ILE B 375 O ALA B 319 SHEET 4 C 4 PHE B 362 SER B 367 -1 N SER B 367 O ASP B 370 SHEET 1 D 5 SER B 310 VAL B 313 0 SHEET 2 D 5 THR B 402 ILE B 406 1 N LYS B 403 O LEU B 311 SHEET 3 D 5 ALA B 384 GLN B 390 -1 N TYR B 386 O THR B 402 SHEET 4 D 5 LEU B 333 GLN B 338 -1 N GLN B 338 O VAL B 385 SHEET 5 D 5 LYS B 345 ILE B 348 -1 N ILE B 348 O TRP B 335 SSBOND 1 CYS A 23 CYS A 88 1555 1555 2.05 SSBOND 2 CYS B 323 CYS B 388 1555 1555 2.04 CISPEP 1 SER A 7 PRO A 8 0 -0.27 CISPEP 2 THR A 94 PRO A 95 0 -0.06 CISPEP 3 SER B 307 PRO B 308 0 0.04 CISPEP 4 THR B 394 PRO B 395 0 -0.37 CRYST1 46.200 54.600 91.400 90.00 90.00 90.00 P 21 21 21 8 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 0.021645 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018315 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010941 0.00000