HEADER BIOTIN-BINDING PROTEIN 11-SEP-97 2RTC TITLE APOSTREPTAVIDIN, PH 3.60, SPACE GROUP I222 COMPND MOL_ID: 1; COMPND 2 MOLECULE: STREPTAVIDIN; COMPND 3 CHAIN: B, D SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES AVIDINII; SOURCE 3 ORGANISM_TAXID: 1895 KEYWDS BIOTIN-BINDING PROTEIN, APOSTREPTAVIDIN, PH 3.60 EXPDTA X-RAY DIFFRACTION AUTHOR B.A.KATZ REVDAT 5 21-FEB-24 2RTC 1 REMARK REVDAT 4 13-JUL-11 2RTC 1 VERSN REVDAT 3 24-FEB-09 2RTC 1 VERSN REVDAT 2 18-NOV-98 2RTC 3 REMARK HETATM KEYWDS REVDAT 1 14-OCT-98 2RTC 0 JRNL AUTH B.A.KATZ JRNL TITL BINDING OF BIOTIN TO STREPTAVIDIN STABILIZES INTERSUBUNIT JRNL TITL 2 SALT BRIDGES BETWEEN ASP61 AND HIS87 AT LOW PH. JRNL REF J.MOL.BIOL. V. 274 776 1997 JRNL REFN ISSN 0022-2836 JRNL PMID 9405158 JRNL DOI 10.1006/JMBI.1997.1444 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH B.A.KATZ,R.T.CASS REMARK 1 TITL IN CRYSTALS OF COMPLEXES OF STREPTAVIDIN WITH PEPTIDE REMARK 1 TITL 2 LIGANDS CONTAINING THE HPQ SEQUENCE THE PKA OF THE PEPTIDE REMARK 1 TITL 3 HISTIDINE IS LESS THAN 3.0 REMARK 1 REF J.BIOL.CHEM. V. 272 13220 1997 REMARK 1 REFN ISSN 0021-9258 REMARK 1 REFERENCE 2 REMARK 1 AUTH B.A.KATZ,B.LIU,R.T.CASS REMARK 1 TITL STRUCTURE-BASED DESIGN TOOLS: STRUCTURAL AND THERMODYNAMIC REMARK 1 TITL 2 COMPARISON WITH BIOTIN OF A SMALL MOLECULE THAT BINDS REMARK 1 TITL 3 STREPTAVIDIN WITH MICROMOLAR AFFINITY REMARK 1 REF J.AM.CHEM.SOC. V. 118 7914 1996 REMARK 1 REFN ISSN 0002-7863 REMARK 1 REFERENCE 3 REMARK 1 AUTH B.A.KATZ REMARK 1 TITL PREPARATION OF A PROTEIN-DIMERIZING LIGAND BY TOPOCHEMISTRY REMARK 1 TITL 2 AND STRUCTURE-BASED DESIGN REMARK 1 REF J.AM.CHEM.SOC. V. 118 2535 1996 REMARK 1 REFN ISSN 0002-7863 REMARK 1 REFERENCE 4 REMARK 1 AUTH B.A.KATZ,R.T.CASS,B.LIU,R.ARZE,N.COLLINS REMARK 1 TITL TOPOCHEMICAL CATALYSIS ACHIEVED BY STRUCTURE-BASED LIGAND REMARK 1 TITL 2 DESIGN REMARK 1 REF J.BIOL.CHEM. V. 270 31210 1995 REMARK 1 REFN ISSN 0021-9258 REMARK 1 REFERENCE 5 REMARK 1 AUTH B.A.KATZ,R.M.STROUD,N.COLLINS,B.LIU,R.ARZE REMARK 1 TITL TOPOCHEMISTRY FOR PREPARING LIGANDS THAT DIMERIZE RECEPTORS REMARK 1 REF CHEM.BIOL. V. 2 591 1995 REMARK 1 REFN ISSN 1074-5521 REMARK 1 REFERENCE 6 REMARK 1 AUTH B.A.KATZ REMARK 1 TITL BINDING TO PROTEIN TARGETS OF PEPTIDIC LEADS DISCOVERED BY REMARK 1 TITL 2 PHAGE DISPLAY: CRYSTAL STRUCTURES OF STREPTAVIDIN-BOUND REMARK 1 TITL 3 LINEAR AND CYCLIC PEPTIDE LIGANDS CONTAINING THE HPQ REMARK 1 TITL 4 SEQUENCE REMARK 1 REF BIOCHEMISTRY V. 34 15421 1995 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 7 REMARK 1 AUTH B.A.KATZ,C.R.JOHNSON,R.T.CASS REMARK 1 TITL STRUCTURE-BASED DESIGN OF HIGH AFFINITY STREPTAVIDIN BINDING REMARK 1 TITL 2 CYCLIC PEPTIDE LIGANDS CONTAINING THIOETHER CROSS-LINKS REMARK 1 REF J.AM.CHEM.SOC. V. 117 8541 1995 REMARK 1 REFN ISSN 0002-7863 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 7.50 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.900 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 60.0 REMARK 3 NUMBER OF REFLECTIONS : 22599 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) : 0.210 REMARK 3 FREE R VALUE : 0.265 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.57 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 27.50 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 : 1819 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 25 REMARK 3 SOLVENT ATOMS : 111 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) : 0.019 REMARK 3 BOND ANGLES (DEGREES) : 4.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.60 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 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: REMARK 3 THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REMARK 3 REFINED: REMARK 3 ALA B 13 REMARK 3 GLU B 14 REMARK 3 ALA B 15 (EXCEPT C AND O), REMARK 3 GLU B 51 (CG, HG1, HG2, CD, OE1, OE2) REMARK 3 ARG B 53 (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22) REMARK 3 ARG B 84 (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22) REMARK 3 GLY B 98 REMARK 3 GLY B 99 REMARK 3 ALA B 100 REMARK 3 GLU B 101 REMARK 3 ALA B 102 REMARK 3 ARG B 103 (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22) REMARK 3 GLU B 116 (CG, HG1, HG2, CD, OE1, OE2) REMARK 3 PRO B 135 REMARK 3 ALA D 13 REMARK 3 GLU D 14 REMARK 3 ALA D 15 REMARK 3 ASP D 36 (CG, OD1, OD2) REMARK 3 ARG D 53 (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22) REMARK 3 ASN D 82 (CG, OD1, ND2, HD21, HD22) REMARK 3 ARG D 84 (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22) REMARK 3 GLU D 101 REMARK 3 ARG D 103 (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22) REMARK 3 GLU D 116 (CG, HG1, HG2, CD, OE1, OE2) REMARK 3 VAL D 133 REMARK 3 REMARK 3 RESIDUES TYR B 60 THROUGH SER B 69 AND TYR D 60 THROUGH SER REMARK 3 D 69 WERE REFINED IN TWO CONFORMATIONS BECAUSE UPON REMARK 3 PROTONATION OF ASP 61 AT LOW PH, ASP 61 UNDERGOES A LARGE REMARK 3 SHIFT IN CONFORMATION AND CHANGE IN HYDROGEN BONDING. THE REMARK 3 LOOPS COMPRISING RESIDUES ASP B 61 THROUGH SER B 69 AND ASP REMARK 3 D 61 THROUGH SER D 69 ALSO UNDERGO CORRESPONDING REMARK 3 CONFORMATIONAL CHANGES. HOWEVER SOME OF THESE RESIDUES ARE REMARK 3 DISORDERED AND NOT VISIBLE IN EITHER CONFORMATION. REMARK 3 REMARK 3 TYR B 22 IS DISORDERED BETWEEN 2 CONFORMATIONS ONE OF WHICH REMARK 3 OCCUPIES A SIMILAR REGION OF SPACE AS A 2-FOLD RELATED B REMARK 3 22. PROPER REFINEMENT WITH XPLOR IS NOT POSSIBLE BECAUSE OF REMARK 3 THE OVERLAP OF ONE CONFORMER WITH THE SYMMETRY RELATED REMARK 3 COUNTERPART. THE FOLLOWING WATERS WERE USED TO ACCOUNT FOR REMARK 3 DENSITY DUE TO THIS CONFORMER OF TYR B 22: HOH 491, HOH REMARK 3 1460, HOH 1465. NO HYDROGENS ARE INCLUDED FOR THESE REMARK 3 "WATERS". REMARK 4 REMARK 4 2RTC 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_1000178589. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 273 REMARK 200 PH : 3.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : BIOTEX (MSC) REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40370 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 : 1.900 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: REJECTION CRITERIA: (I(H)I - ) > [0.30 * () + 0.10*I(H)I], WHERE I(H)I IS THE ITH OBSERVATION OF THE REMARK 200 INTENSITY OF REFLECTION H (M.G.ROSSMANN, A.G.W.LESLIE, S.S.ABDEL- REMARK 200 MEGUID, T.TSUKIHARA, J.APPL.CRYST. 12, 570 - 581). THIS REMARK 200 REJECTION CRITERION IS THE DEFAULT OF THE MSC PROGRAM BIOTEX. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 20.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SYNTHETIC MOTHER LIQUOR OF 75% REMARK 280 SATURATED AMMONIUM SULFATE, SODIUM FORMATE ADJUSTED TO PH 3.60. REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 47.59000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 52.69500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 23.94500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 47.59000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 52.69500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 23.94500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 47.59000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 52.69500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 23.94500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 47.59000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 52.69500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 23.94500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11310 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -262.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D 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 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 ASP B 1 REMARK 465 PRO B 2 REMARK 465 SER B 3 REMARK 465 LYS B 4 REMARK 465 ASP B 5 REMARK 465 SER B 6 REMARK 465 LYS B 7 REMARK 465 ALA B 8 REMARK 465 GLN B 9 REMARK 465 VAL B 10 REMARK 465 SER B 11 REMARK 465 ALA B 12 REMARK 465 ASP D 1 REMARK 465 PRO D 2 REMARK 465 SER D 3 REMARK 465 LYS D 4 REMARK 465 ASP D 5 REMARK 465 SER D 6 REMARK 465 LYS D 7 REMARK 465 ALA D 8 REMARK 465 GLN D 9 REMARK 465 VAL D 10 REMARK 465 SER D 11 REMARK 465 ALA D 12 REMARK 465 LYS D 134 REMARK 465 PRO D 135 REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 GLU B 14 REMARK 475 ALA D 15 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 PRO B 64 N CA C O CB CG CD REMARK 480 ALA B 65 N CA C O CB REMARK 480 GLU B 116 CG CD OE1 OE2 REMARK 480 GLU D 14 CB CG CD OE1 OE2 REMARK 480 ALA D 63 N CA C O CB REMARK 480 PRO D 64 N CA C O CB CG CD REMARK 480 ALA D 65 N CA C O CB REMARK 480 THR D 66 N CA C O CB OG1 CG2 REMARK 480 GLU D 101 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 HE21 GLN B 95 H THR D 114 1.28 REMARK 500 H THR B 114 HE21 GLN D 95 1.32 REMARK 500 HD2 ASP B 61 OD1 ASN D 85 1.41 REMARK 500 O ALA D 102 H1 HOH D 635 1.50 REMARK 500 O2 SO4 D 402 H2 HOH D 503 1.51 REMARK 500 OG1 THR D 40 H2 HOH D 602 1.52 REMARK 500 O TYR D 60 H2 HOH D 636 1.55 REMARK 500 O4 SO4 D 402 H1 HOH D 503 1.56 REMARK 500 O TYR D 60 H2 HOH D 636 1.56 REMARK 500 O GLY D 99 H2 HOH D 633 1.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH B 491 O HOH B 491 3655 0.51 REMARK 500 O HOH D 1465 O HOH D 1465 3556 0.82 REMARK 500 O HOH B 491 O HOH D 1465 8555 1.39 REMARK 500 O HOH B 1460 O HOH B 1460 3655 1.42 REMARK 500 O HOH B 1460 O HOH D 1465 8555 1.99 REMARK 500 REMARK 500 REMARK: NULL 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 HIS B 87 NE2 HIS B 87 CD2 -0.075 REMARK 500 HIS B 127 NE2 HIS B 127 CD2 -0.075 REMARK 500 SER D 45 CA SER D 45 CB 0.098 REMARK 500 HIS D 87 NE2 HIS D 87 CD2 -0.068 REMARK 500 HIS D 87 NE2 HIS D 87 CD2 -0.071 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 TRP B 21 CG - CD1 - NE1 ANGL. DEV. = -6.8 DEGREES REMARK 500 TRP B 21 CD1 - NE1 - CE2 ANGL. DEV. = 8.9 DEGREES REMARK 500 TRP B 21 NE1 - CE2 - CZ2 ANGL. DEV. = 8.5 DEGREES REMARK 500 TRP B 21 NE1 - CE2 - CD2 ANGL. DEV. = -6.6 DEGREES REMARK 500 TRP B 75 CG - CD1 - NE1 ANGL. DEV. = -8.1 DEGREES REMARK 500 TRP B 75 CD1 - NE1 - CE2 ANGL. DEV. = 8.9 DEGREES REMARK 500 TRP B 75 NE1 - CE2 - CZ2 ANGL. DEV. = 7.0 DEGREES REMARK 500 ALA B 78 N - CA - C ANGL. DEV. = -18.1 DEGREES REMARK 500 TRP B 79 CG - CD1 - NE1 ANGL. DEV. = -7.5 DEGREES REMARK 500 TRP B 79 CD1 - NE1 - CE2 ANGL. DEV. = 7.4 DEGREES REMARK 500 TRP B 79 NE1 - CE2 - CZ2 ANGL. DEV. = 7.2 DEGREES REMARK 500 TRP B 92 CG - CD1 - NE1 ANGL. DEV. = -8.4 DEGREES REMARK 500 TRP B 92 CD1 - NE1 - CE2 ANGL. DEV. = 9.0 DEGREES REMARK 500 GLN B 107 CA - CB - CG ANGL. DEV. = -13.7 DEGREES REMARK 500 TRP B 108 CB - CG - CD2 ANGL. DEV. = 8.7 DEGREES REMARK 500 TRP B 108 CG - CD1 - NE1 ANGL. DEV. = -6.0 DEGREES REMARK 500 TRP B 108 CD1 - NE1 - CE2 ANGL. DEV. = 9.0 DEGREES REMARK 500 TRP B 108 NE1 - CE2 - CZ2 ANGL. DEV. = 9.2 DEGREES REMARK 500 TRP B 108 NE1 - CE2 - CD2 ANGL. DEV. = -7.1 DEGREES REMARK 500 TRP B 108 CE2 - CD2 - CG ANGL. DEV. = 5.0 DEGREES REMARK 500 TRP B 108 CG - CD2 - CE3 ANGL. DEV. = -6.9 DEGREES REMARK 500 TRP B 120 CG - CD1 - NE1 ANGL. DEV. = -7.1 DEGREES REMARK 500 TRP B 120 CD1 - NE1 - CE2 ANGL. DEV. = 8.0 DEGREES REMARK 500 TRP B 120 NE1 - CE2 - CZ2 ANGL. DEV. = 8.3 DEGREES REMARK 500 TRP D 21 CG - CD1 - NE1 ANGL. DEV. = -7.0 DEGREES REMARK 500 TRP D 21 CD1 - NE1 - CE2 ANGL. DEV. = 8.1 DEGREES REMARK 500 TRP D 21 NE1 - CE2 - CZ2 ANGL. DEV. = 7.8 DEGREES REMARK 500 ARG D 59 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 TRP D 75 CG - CD1 - NE1 ANGL. DEV. = -8.1 DEGREES REMARK 500 TRP D 75 CD1 - NE1 - CE2 ANGL. DEV. = 9.0 DEGREES REMARK 500 TRP D 75 NE1 - CE2 - CZ2 ANGL. DEV. = 8.2 DEGREES REMARK 500 TRP D 75 NE1 - CE2 - CD2 ANGL. DEV. = -6.4 DEGREES REMARK 500 ALA D 78 N - CA - C ANGL. DEV. = -18.1 DEGREES REMARK 500 TRP D 79 CG - CD1 - NE1 ANGL. DEV. = -6.5 DEGREES REMARK 500 TRP D 79 CD1 - NE1 - CE2 ANGL. DEV. = 7.1 DEGREES REMARK 500 TRP D 79 NE1 - CE2 - CZ2 ANGL. DEV. = 7.3 DEGREES REMARK 500 ARG D 84 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 TRP D 92 CG - CD1 - NE1 ANGL. DEV. = -8.4 DEGREES REMARK 500 TRP D 92 CD1 - NE1 - CE2 ANGL. DEV. = 9.7 DEGREES REMARK 500 TRP D 92 NE1 - CE2 - CZ2 ANGL. DEV. = 8.2 DEGREES REMARK 500 TRP D 92 NE1 - CE2 - CD2 ANGL. DEV. = -6.2 DEGREES REMARK 500 GLN D 107 N - CA - C ANGL. DEV. = -16.2 DEGREES REMARK 500 TRP D 108 CG - CD1 - NE1 ANGL. DEV. = -8.2 DEGREES REMARK 500 TRP D 108 CD1 - NE1 - CE2 ANGL. DEV. = 9.2 DEGREES REMARK 500 TRP D 108 NE1 - CE2 - CZ2 ANGL. DEV. = 7.6 DEGREES REMARK 500 TRP D 120 CG - CD1 - NE1 ANGL. DEV. = -7.4 DEGREES REMARK 500 TRP D 120 CD1 - NE1 - CE2 ANGL. DEV. = 8.8 DEGREES REMARK 500 TRP D 120 NE1 - CE2 - CZ2 ANGL. DEV. = 8.1 DEGREES REMARK 500 TRP D 120 NE1 - CE2 - CD2 ANGL. DEV. = -6.5 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 B 52 -156.99 93.11 REMARK 500 SER B 62 105.62 -51.71 REMARK 500 PRO B 64 80.42 -48.12 REMARK 500 PRO B 64 -167.97 -59.54 REMARK 500 ALA B 65 62.10 -115.21 REMARK 500 THR B 66 44.57 -79.99 REMARK 500 VAL B 133 -64.60 -122.37 REMARK 500 GLU D 14 -146.30 43.89 REMARK 500 ALA D 15 -65.19 1.14 REMARK 500 GLU D 51 100.71 -168.24 REMARK 500 SER D 52 -156.69 96.36 REMARK 500 ALA D 65 53.69 -150.47 REMARK 500 THR D 66 54.56 -93.12 REMARK 500 ASP D 67 20.76 -65.76 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ALA B 63 PRO B 64 135.32 REMARK 500 ALA D 63 PRO D 64 145.73 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG B 53 0.13 SIDE CHAIN REMARK 500 ARG B 103 0.17 SIDE CHAIN REMARK 500 ARG D 53 0.20 SIDE CHAIN REMARK 500 ARG D 103 0.15 SIDE CHAIN 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 D 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 D 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 D 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 404 DBREF 2RTC B 1 135 UNP P22629 SAV_STRAV 25 159 DBREF 2RTC D 1 135 UNP P22629 SAV_STRAV 25 159 SEQRES 1 B 135 ASP PRO SER LYS ASP SER LYS ALA GLN VAL SER ALA ALA SEQRES 2 B 135 GLU ALA GLY ILE THR GLY THR TRP TYR ASN GLN LEU GLY SEQRES 3 B 135 SER THR PHE ILE VAL THR ALA GLY ALA ASP GLY ALA LEU SEQRES 4 B 135 THR GLY THR TYR GLU SER ALA VAL GLY ASN ALA GLU SER SEQRES 5 B 135 ARG TYR VAL LEU THR GLY ARG TYR ASP SER ALA PRO ALA SEQRES 6 B 135 THR ASP GLY SER GLY THR ALA LEU GLY TRP THR VAL ALA SEQRES 7 B 135 TRP LYS ASN ASN TYR ARG ASN ALA HIS SER ALA THR THR SEQRES 8 B 135 TRP SER GLY GLN TYR VAL GLY GLY ALA GLU ALA ARG ILE SEQRES 9 B 135 ASN THR GLN TRP LEU LEU THR SER GLY THR THR GLU ALA SEQRES 10 B 135 ASN ALA TRP LYS SER THR LEU VAL GLY HIS ASP THR PHE SEQRES 11 B 135 THR LYS VAL LYS PRO SEQRES 1 D 135 ASP PRO SER LYS ASP SER LYS ALA GLN VAL SER ALA ALA SEQRES 2 D 135 GLU ALA GLY ILE THR GLY THR TRP TYR ASN GLN LEU GLY SEQRES 3 D 135 SER THR PHE ILE VAL THR ALA GLY ALA ASP GLY ALA LEU SEQRES 4 D 135 THR GLY THR TYR GLU SER ALA VAL GLY ASN ALA GLU SER SEQRES 5 D 135 ARG TYR VAL LEU THR GLY ARG TYR ASP SER ALA PRO ALA SEQRES 6 D 135 THR ASP GLY SER GLY THR ALA LEU GLY TRP THR VAL ALA SEQRES 7 D 135 TRP LYS ASN ASN TYR ARG ASN ALA HIS SER ALA THR THR SEQRES 8 D 135 TRP SER GLY GLN TYR VAL GLY GLY ALA GLU ALA ARG ILE SEQRES 9 D 135 ASN THR GLN TRP LEU LEU THR SER GLY THR THR GLU ALA SEQRES 10 D 135 ASN ALA TRP LYS SER THR LEU VAL GLY HIS ASP THR PHE SEQRES 11 D 135 THR LYS VAL LYS PRO HET SO4 B 403 5 HET SO4 B 404 5 HET SO4 D 400 5 HET SO4 D 401 5 HET SO4 D 402 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 5(O4 S 2-) FORMUL 8 HOH *111(H2 O) HELIX 1 1 GLU B 14 ILE B 17 1 4 HELIX 2 2 ALA B 119 LYS B 121 5 3 HELIX 3 3 GLU D 14 ILE D 17 5 4 HELIX 4 4 GLU D 116 LYS D 121 5 6 SHEET 1 A 9 GLY B 19 TYR B 22 0 SHEET 2 A 9 THR B 28 ALA B 33 -1 N VAL B 31 O GLY B 19 SHEET 3 A 9 ALA B 38 GLU B 44 -1 N GLU B 44 O THR B 28 SHEET 4 A 9 ARG B 53 TYR B 60 -1 N GLY B 58 O LEU B 39 SHEET 5 A 9 THR B 71 ALA B 78 -1 N THR B 76 O THR B 57 SHEET 6 A 9 SER B 88 VAL B 97 -1 N TYR B 96 O THR B 71 SHEET 7 A 9 ARG B 103 SER B 112 -1 N THR B 111 O ALA B 89 SHEET 8 A 9 THR B 123 LYS B 134 -1 N PHE B 130 O ILE B 104 SHEET 9 A 9 THR B 20 ASN B 23 -1 N TYR B 22 O THR B 131 SHEET 1 B 8 GLY D 19 TYR D 22 0 SHEET 2 B 8 THR D 28 ALA D 33 -1 N VAL D 31 O GLY D 19 SHEET 3 B 8 ALA D 38 GLU D 44 -1 N GLU D 44 O THR D 28 SHEET 4 B 8 ARG D 53 TYR D 60 -1 N GLY D 58 O LEU D 39 SHEET 5 B 8 THR D 71 ALA D 78 -1 N THR D 76 O THR D 57 SHEET 6 B 8 SER D 88 VAL D 97 -1 N TYR D 96 O THR D 71 SHEET 7 B 8 ARG D 103 SER D 112 -1 N THR D 111 O ALA D 89 SHEET 8 B 8 THR D 123 PHE D 130 -1 N PHE D 130 O ILE D 104 SITE 1 AC1 3 ASN D 49 SO4 D 401 SO4 D 402 SITE 1 AC2 5 TRP B 120 GLY D 48 ASN D 49 SO4 D 400 SITE 2 AC2 5 SO4 D 402 SITE 1 AC3 9 TRP B 120 GLY D 48 ASN D 49 TRP D 79 SITE 2 AC3 9 SER D 88 LEU D 110 SO4 D 400 SO4 D 401 SITE 3 AC3 9 HOH D 503 SITE 1 AC4 8 ASN B 23 LEU B 25 TYR B 43 SER B 45 SITE 2 AC4 8 TRP B 92 ASP B 128 HOH B 507 HOH B1464 SITE 1 AC5 5 ASN B 49 ALA B 86 SER B 88 LEU B 110 SITE 2 AC5 5 HOH B 506 CRYST1 95.180 105.390 47.890 90.00 90.00 90.00 I 2 2 2 16 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 0.010506 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009489 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020881 0.00000 MTRIX1 1 -0.999962 -0.016449 -0.002489 51.98730 1 MTRIX2 1 -0.013581 0.720683 0.693131 0.44530 1 MTRIX3 1 -0.009608 0.693069 -0.720807 0.27230 1