HEADER UNKNOWN FUNCTION 22-JAN-03 1NQN TITLE STRUCTURE OF AVM-W110K (W110K MUTANT OF AVIDIN) COMPND MOL_ID: 1; COMPND 2 MOLECULE: AVIDIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 3 ORGANISM_COMMON: CHICKEN; SOURCE 4 ORGANISM_TAXID: 9031; SOURCE 5 GENE: AVD; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: JM109; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS AVIDIN, STREPTAVIDIN, BIOTIN, MONOMER-MONOMER INTERACTION, UNKNOWN KEYWDS 2 FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR Y.PAZY,Y.EISENBERG-DOMOVICH,O.H.LAITINEN,M.S.KULOMAA,E.A.BAYER, AUTHOR 2 M.WILCHEK,O.LIVNAH REVDAT 6 09-OCT-24 1NQN 1 REMARK REVDAT 5 27-OCT-21 1NQN 1 SEQADV REVDAT 4 31-JAN-18 1NQN 1 REMARK REVDAT 3 24-FEB-09 1NQN 1 VERSN REVDAT 2 22-JUL-03 1NQN 1 TITLE REVDAT 1 15-JUL-03 1NQN 0 JRNL AUTH Y.PAZY,Y.EISENBERG-DOMOVICH,O.H.LAITINEN,M.S.KULOMAA, JRNL AUTH 2 E.A.BAYER,M.WILCHEK,O.LIVNAH JRNL TITL DIMER-TETRAMER TRANSITION BETWEEN SOLUTION AND CRYSTALLINE JRNL TITL 2 STATES OF STREPTAVIDIN AND AVIDIN MUTANTS. JRNL REF J.BACTERIOL. V. 185 4050 2003 JRNL REFN ISSN 0021-9193 JRNL PMID 12837778 JRNL DOI 10.1128/JB.185.14.4050-4056.2003 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 21282 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1797 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 94 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1NQN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-FEB-03. REMARK 100 THE DEPOSITION ID IS D_1000018117. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JUN-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.93 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD 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 : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 32% MPEG 2K, 0.1M TRIS-HCL, PH 8.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 20K, TEMPERATURE REMARK 280 293.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 33.85150 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.72500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.85150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.72500 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: TETRAMERIC 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 67.70300 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 77.45000 REMARK 350 BIOMT3 2 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 THR A 38 REMARK 465 ALA A 39 REMARK 465 THR A 40 REMARK 465 SER A 41 REMARK 465 ARG B 202 REMARK 465 ALA B 236 REMARK 465 VAL B 237 REMARK 465 THR B 238 REMARK 465 ALA B 239 REMARK 465 THR B 240 REMARK 465 SER B 241 REMARK 465 ASN B 242 REMARK 465 GLU B 243 REMARK 465 ILE B 244 REMARK 465 ARG B 287 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 LEU B 249 CA - CB - CG ANGL. DEV. = 18.9 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 GLU A 43 93.68 -52.62 REMARK 500 LYS A 58 51.57 39.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1NQM RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 ACCORDING TO SWISS-PROT ENTRY P02701 REMARK 999 THERE IS A VARIANT IN RESIDUE 58 REMARK 999 ILE -> THR (IN APPR. 50% OF THE CHAINS). DBREF 1NQN A 2 123 UNP P02701 AVID_CHICK 26 147 DBREF 1NQN B 202 323 UNP P02701 AVID_CHICK 26 147 SEQADV 1NQN THR A 34 UNP P02701 ILE 58 SEE REMARK 999 SEQADV 1NQN LYS A 110 UNP P02701 TRP 134 ENGINEERED MUTATION SEQADV 1NQN THR B 234 UNP P02701 ILE 58 SEE REMARK 999 SEQADV 1NQN LYS B 310 UNP P02701 TRP 134 ENGINEERED MUTATION SEQRES 1 A 122 ARG LYS CYS SER LEU THR GLY LYS TRP THR ASN ASP LEU SEQRES 2 A 122 GLY SER ASN MET THR ILE GLY ALA VAL ASN SER ARG GLY SEQRES 3 A 122 GLU PHE THR GLY THR TYR THR THR ALA VAL THR ALA THR SEQRES 4 A 122 SER ASN GLU ILE LYS GLU SER PRO LEU HIS GLY THR GLU SEQRES 5 A 122 ASN THR ILE ASN LYS ARG THR GLN PRO THR PHE GLY PHE SEQRES 6 A 122 THR VAL ASN TRP LYS PHE SER GLU SER THR THR VAL PHE SEQRES 7 A 122 THR GLY GLN CYS PHE ILE ASP ARG ASN GLY LYS GLU VAL SEQRES 8 A 122 LEU LYS THR MET TRP LEU LEU ARG SER SER VAL ASN ASP SEQRES 9 A 122 ILE GLY ASP ASP LYS LYS ALA THR ARG VAL GLY ILE ASN SEQRES 10 A 122 ILE PHE THR ARG LEU SEQRES 1 B 122 ARG LYS CYS SER LEU THR GLY LYS TRP THR ASN ASP LEU SEQRES 2 B 122 GLY SER ASN MET THR ILE GLY ALA VAL ASN SER ARG GLY SEQRES 3 B 122 GLU PHE THR GLY THR TYR THR THR ALA VAL THR ALA THR SEQRES 4 B 122 SER ASN GLU ILE LYS GLU SER PRO LEU HIS GLY THR GLU SEQRES 5 B 122 ASN THR ILE ASN LYS ARG THR GLN PRO THR PHE GLY PHE SEQRES 6 B 122 THR VAL ASN TRP LYS PHE SER GLU SER THR THR VAL PHE SEQRES 7 B 122 THR GLY GLN CYS PHE ILE ASP ARG ASN GLY LYS GLU VAL SEQRES 8 B 122 LEU LYS THR MET TRP LEU LEU ARG SER SER VAL ASN ASP SEQRES 9 B 122 ILE GLY ASP ASP LYS LYS ALA THR ARG VAL GLY ILE ASN SEQRES 10 B 122 ILE PHE THR ARG LEU FORMUL 3 HOH *94(H2 O) HELIX 1 1 ASP A 105 LYS A 111 5 7 HELIX 2 2 ASP B 305 LYS B 311 5 7 SHEET 1 A 9 GLY A 8 THR A 11 0 SHEET 2 A 9 ASN A 17 ILE A 20 -1 O MET A 18 N TRP A 10 SHEET 3 A 9 GLU A 28 ALA A 36 -1 O THR A 34 N ASN A 17 SHEET 4 A 9 ILE A 44 GLU A 53 -1 O SER A 47 N TYR A 33 SHEET 5 A 9 THR A 63 VAL A 68 -1 O GLY A 65 N THR A 52 SHEET 6 A 9 THR A 76 ILE A 85 -1 O THR A 77 N VAL A 68 SHEET 7 A 9 GLU A 91 ARG A 100 -1 O ARG A 100 N THR A 76 SHEET 8 A 9 THR A 113 ARG A 122 -1 O GLY A 116 N TRP A 97 SHEET 9 A 9 GLY A 8 THR A 11 -1 N THR A 11 O THR A 121 SHEET 1 B 9 GLY B 208 THR B 211 0 SHEET 2 B 9 ASN B 217 ILE B 220 -1 O MET B 218 N TRP B 210 SHEET 3 B 9 GLU B 228 THR B 234 -1 O THR B 234 N ASN B 217 SHEET 4 B 9 SER B 247 GLU B 253 -1 O GLY B 251 N PHE B 229 SHEET 5 B 9 THR B 263 VAL B 268 -1 O THR B 267 N HIS B 250 SHEET 6 B 9 THR B 276 ILE B 285 -1 O THR B 277 N VAL B 268 SHEET 7 B 9 GLU B 291 ARG B 300 -1 O ARG B 300 N THR B 276 SHEET 8 B 9 THR B 313 ARG B 322 -1 O GLY B 316 N TRP B 297 SHEET 9 B 9 GLY B 208 THR B 211 -1 N THR B 211 O THR B 321 SSBOND 1 CYS A 4 CYS A 83 1555 1555 2.02 SSBOND 2 CYS B 204 CYS B 283 1555 1555 2.05 CRYST1 67.703 77.450 42.894 90.00 90.00 90.00 P 21 21 2 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 0.014770 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012912 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023313 0.00000