HEADER DE NOVO PROTEIN 26-JAN-11 3QHT TITLE CRYSTAL STRUCTURE OF THE MONOBODY YSMB-1 BOUND TO YEAST SUMO COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-LIKE PROTEIN SMT3; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: YEAST SMALL UBIQUITIN-LIKE MODIFIER (SUMO); COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: MONOBODY YSMB-1; COMPND 8 CHAIN: C, D; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: SMT3, YDR510W, D9719.15; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: ARTIFICIAL GENE; SOURCE 10 ORGANISM_TAXID: 32630; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS FIBRONECTIN TYPE III, YEAST SMALL UBIQUITIN-LIKE MODIFIER, SMT3, DE KEYWDS 2 NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.KOIDE,R.N.GILBRETH REVDAT 4 13-SEP-23 3QHT 1 REMARK DBREF SEQADV REVDAT 3 08-NOV-17 3QHT 1 REMARK REVDAT 2 25-MAY-11 3QHT 1 JRNL REVDAT 1 11-MAY-11 3QHT 0 JRNL AUTH R.N.GILBRETH,K.TRUONG,I.MADU,A.KOIDE,J.B.WOJCIK,N.S.LI, JRNL AUTH 2 J.A.PICCIRILLI,Y.CHEN,S.KOIDE JRNL TITL ISOFORM-SPECIFIC MONOBODY INHIBITORS OF SMALL JRNL TITL 2 UBIQUITIN-RELATED MODIFIERS ENGINEERED USING JRNL TITL 3 STRUCTURE-GUIDED LIBRARY DESIGN. JRNL REF PROC.NATL.ACAD.SCI.USA V. 108 7751 2011 JRNL REFN ISSN 0027-8424 JRNL PMID 21518904 JRNL DOI 10.1073/PNAS.1102294108 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 21341 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 + TEST SET) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.223 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1151 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1450 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.29 REMARK 3 BIN R VALUE (WORKING SET) : 0.2470 REMARK 3 BIN FREE R VALUE SET COUNT : 81 REMARK 3 BIN FREE R VALUE : 0.3560 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2666 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 48 REMARK 3 SOLVENT ATOMS : 85 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.82 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.67000 REMARK 3 B22 (A**2) : -0.03000 REMARK 3 B33 (A**2) : 0.70000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.287 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.240 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.171 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 14.399 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.925 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.896 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2777 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3759 ; 1.864 ; 1.978 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 336 ; 7.806 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 121 ;33.575 ;23.636 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 449 ;19.323 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;18.328 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 413 ; 0.160 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2084 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1185 ; 0.232 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1898 ; 0.308 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 142 ; 0.158 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 54 ; 0.270 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 12 ; 0.140 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1733 ; 1.107 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2752 ; 1.923 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1203 ; 2.568 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1007 ; 3.918 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3QHT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-JAN-11. REMARK 100 THE DEPOSITION ID IS D_1000063662. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-NOV-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 REMARK 200 MONOCHROMATOR : C(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22586 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.3 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : 0.64300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.150 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRIES 1FNA AND 2EKE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 14% PEG8000, 16% GLYCEROL, PH 8.0, REMARK 280 VAPOR DIFFUSION, TEMPERATURE 292K 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 29.81850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 87.73100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.81850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 87.73100 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 2810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9280 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 REMARK 350 BIOMOLECULE: 2 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: 1470 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 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 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 GLY A 1 REMARK 465 SER A 2 REMARK 465 ASP A 3 REMARK 465 SER A 4 REMARK 465 GLU A 5 REMARK 465 VAL A 6 REMARK 465 ASN A 7 REMARK 465 GLN A 8 REMARK 465 GLU A 9 REMARK 465 ALA A 10 REMARK 465 LYS A 11 REMARK 465 PRO A 12 REMARK 465 GLU A 13 REMARK 465 VAL A 14 REMARK 465 LYS A 15 REMARK 465 PRO A 16 REMARK 465 GLU A 17 REMARK 465 VAL A 18 REMARK 465 GLY A 98 REMARK 465 GLY B 1 REMARK 465 SER B 2 REMARK 465 ASP B 3 REMARK 465 SER B 4 REMARK 465 GLU B 5 REMARK 465 VAL B 6 REMARK 465 ASN B 7 REMARK 465 GLN B 8 REMARK 465 GLU B 9 REMARK 465 ALA B 10 REMARK 465 LYS B 11 REMARK 465 PRO B 12 REMARK 465 GLU B 13 REMARK 465 VAL B 14 REMARK 465 LYS B 15 REMARK 465 PRO B 16 REMARK 465 GLU B 17 REMARK 465 VAL B 18 REMARK 465 LYS B 19 REMARK 465 PRO B 20 REMARK 465 GLU B 21 REMARK 465 GLN B 95 REMARK 465 ILE B 96 REMARK 465 GLY B 97 REMARK 465 GLY B 98 REMARK 465 GLY C -2 REMARK 465 SER C -1 REMARK 465 SER C 0 REMARK 465 VAL C 1 REMARK 465 GLY D -2 REMARK 465 SER D -1 REMARK 465 SER D 0 REMARK 465 VAL D 1 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 ILE A 96 CB CG1 CG2 CD1 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 VAL D 4 C - N - CA ANGL. DEV. = 16.0 DEGREES REMARK 500 SER D 28 C - N - CA ANGL. DEV. = 17.7 DEGREES REMARK 500 SER D 28 N - CA - CB ANGL. DEV. = 9.9 DEGREES REMARK 500 LEU D 81 CA - CB - CG ANGL. DEV. = 17.6 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 ASN A 86 11.81 80.15 REMARK 500 GLU A 94 116.27 77.52 REMARK 500 GLN A 95 94.15 74.57 REMARK 500 ILE A 96 -142.24 -73.03 REMARK 500 HIS B 23 111.24 70.59 REMARK 500 SER B 32 -63.42 -98.90 REMARK 500 GLN B 56 1.87 168.71 REMARK 500 ARG B 93 -88.39 -40.66 REMARK 500 ARG B 93 -88.39 -43.70 REMARK 500 SER C 3 119.22 38.71 REMARK 500 ALA C 24 42.40 -107.79 REMARK 500 ASN C 42 32.16 -63.94 REMARK 500 TYR C 79 -117.97 45.67 REMARK 500 VAL D 4 79.32 90.31 REMARK 500 SER D 28 -63.86 124.66 REMARK 500 SER D 43 151.49 179.43 REMARK 500 TYR D 79 -118.33 52.72 REMARK 500 SER D 86 74.41 41.16 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 PRO A 20 GLU A 21 61.36 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 GOL A 99 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 100 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL C 95 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL C 96 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL C 97 DBREF 3QHT A 2 98 UNP Q12306 SMT3_YEAST 2 98 DBREF 3QHT B 2 98 UNP Q12306 SMT3_YEAST 2 98 DBREF 3QHT C -2 94 PDB 3QHT 3QHT -2 94 DBREF 3QHT D -2 94 PDB 3QHT 3QHT -2 94 SEQADV 3QHT GLY A 1 UNP Q12306 EXPRESSION TAG SEQADV 3QHT GLY B 1 UNP Q12306 EXPRESSION TAG SEQRES 1 A 98 GLY SER ASP SER GLU VAL ASN GLN GLU ALA LYS PRO GLU SEQRES 2 A 98 VAL LYS PRO GLU VAL LYS PRO GLU THR HIS ILE ASN LEU SEQRES 3 A 98 LYS VAL SER ASP GLY SER SER GLU ILE PHE PHE LYS ILE SEQRES 4 A 98 LYS LYS THR THR PRO LEU ARG ARG LEU MET GLU ALA PHE SEQRES 5 A 98 ALA LYS ARG GLN GLY LYS GLU MET ASP SER LEU ARG PHE SEQRES 6 A 98 LEU TYR ASP GLY ILE ARG ILE GLN ALA ASP GLN THR PRO SEQRES 7 A 98 GLU ASP LEU ASP MET GLU ASP ASN ASP ILE ILE GLU ALA SEQRES 8 A 98 HIS ARG GLU GLN ILE GLY GLY SEQRES 1 B 98 GLY SER ASP SER GLU VAL ASN GLN GLU ALA LYS PRO GLU SEQRES 2 B 98 VAL LYS PRO GLU VAL LYS PRO GLU THR HIS ILE ASN LEU SEQRES 3 B 98 LYS VAL SER ASP GLY SER SER GLU ILE PHE PHE LYS ILE SEQRES 4 B 98 LYS LYS THR THR PRO LEU ARG ARG LEU MET GLU ALA PHE SEQRES 5 B 98 ALA LYS ARG GLN GLY LYS GLU MET ASP SER LEU ARG PHE SEQRES 6 B 98 LEU TYR ASP GLY ILE ARG ILE GLN ALA ASP GLN THR PRO SEQRES 7 B 98 GLU ASP LEU ASP MET GLU ASP ASN ASP ILE ILE GLU ALA SEQRES 8 B 98 HIS ARG GLU GLN ILE GLY GLY SEQRES 1 C 97 GLY SER SER VAL SER SER VAL PRO THR LYS LEU GLU VAL SEQRES 2 C 97 VAL ALA ALA THR PRO THR SER LEU LEU ILE SER TRP ASP SEQRES 3 C 97 ALA SER SER SER SER VAL SER TYR TYR ARG ILE THR TYR SEQRES 4 C 97 GLY GLU THR GLY GLY ASN SER PRO VAL GLN GLU PHE THR SEQRES 5 C 97 VAL PRO GLY SER SER SER THR ALA THR ILE SER GLY LEU SEQRES 6 C 97 SER PRO GLY VAL ASP TYR THR ILE THR VAL TYR ALA TYR SEQRES 7 C 97 TYR SER TYR TYR ASP LEU TYR TYR SER TYR SER PRO SER SEQRES 8 C 97 SER ILE ASN TYR ARG THR SEQRES 1 D 97 GLY SER SER VAL SER SER VAL PRO THR LYS LEU GLU VAL SEQRES 2 D 97 VAL ALA ALA THR PRO THR SER LEU LEU ILE SER TRP ASP SEQRES 3 D 97 ALA SER SER SER SER VAL SER TYR TYR ARG ILE THR TYR SEQRES 4 D 97 GLY GLU THR GLY GLY ASN SER PRO VAL GLN GLU PHE THR SEQRES 5 D 97 VAL PRO GLY SER SER SER THR ALA THR ILE SER GLY LEU SEQRES 6 D 97 SER PRO GLY VAL ASP TYR THR ILE THR VAL TYR ALA TYR SEQRES 7 D 97 TYR SER TYR TYR ASP LEU TYR TYR SER TYR SER PRO SER SEQRES 8 D 97 SER ILE ASN TYR ARG THR HET GOL A 99 6 HET GOL A 100 6 HET GOL A 101 6 HET GOL A 102 6 HET GOL A 103 6 HET GOL C 95 6 HET GOL C 96 6 HET GOL C 97 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 GOL 8(C3 H8 O3) FORMUL 13 HOH *85(H2 O) HELIX 1 1 LEU A 45 GLN A 56 1 12 HELIX 2 2 GLU A 59 ASP A 61 5 3 HELIX 3 3 LEU B 45 ARG B 55 1 11 HELIX 4 4 GLU B 59 LEU B 63 5 5 SHEET 1 A 9 ILE A 70 ARG A 71 0 SHEET 2 A 9 LEU A 63 TYR A 67 -1 N TYR A 67 O ILE A 70 SHEET 3 A 9 ASP A 87 ARG A 93 -1 O GLU A 90 N LEU A 66 SHEET 4 A 9 HIS A 23 SER A 29 1 N SER A 29 O ALA A 91 SHEET 5 A 9 GLU A 34 LYS A 40 -1 O ILE A 39 N ILE A 24 SHEET 6 A 9 LEU C 81 SER C 84 -1 O TYR C 82 N LYS A 38 SHEET 7 A 9 ASP C 67 TYR C 78 -1 N TYR C 76 O TYR C 83 SHEET 8 A 9 TYR C 31 GLU C 38 -1 N TYR C 31 O TYR C 75 SHEET 9 A 9 GLN C 46 PRO C 51 -1 O PHE C 48 N ILE C 34 SHEET 1 B 8 ILE A 70 ARG A 71 0 SHEET 2 B 8 LEU A 63 TYR A 67 -1 N TYR A 67 O ILE A 70 SHEET 3 B 8 ASP A 87 ARG A 93 -1 O GLU A 90 N LEU A 66 SHEET 4 B 8 HIS A 23 SER A 29 1 N SER A 29 O ALA A 91 SHEET 5 B 8 GLU A 34 LYS A 40 -1 O ILE A 39 N ILE A 24 SHEET 6 B 8 LEU C 81 SER C 84 -1 O TYR C 82 N LYS A 38 SHEET 7 B 8 ASP C 67 TYR C 78 -1 N TYR C 76 O TYR C 83 SHEET 8 B 8 SER C 88 ARG C 93 -1 O ILE C 90 N ILE C 70 SHEET 1 C 9 ILE B 70 ARG B 71 0 SHEET 2 C 9 ARG B 64 TYR B 67 -1 N TYR B 67 O ILE B 70 SHEET 3 C 9 ASP B 87 HIS B 92 -1 O HIS B 92 N ARG B 64 SHEET 4 C 9 ILE B 24 SER B 29 1 N SER B 29 O ALA B 91 SHEET 5 C 9 GLU B 34 ILE B 39 -1 O PHE B 37 N LEU B 26 SHEET 6 C 9 LEU D 81 TYR D 85 -1 O SER D 84 N PHE B 36 SHEET 7 C 9 ASP D 67 TYR D 78 -1 N TYR D 76 O TYR D 83 SHEET 8 C 9 TYR D 31 GLU D 38 -1 N TYR D 31 O TYR D 75 SHEET 9 C 9 GLN D 46 PRO D 51 -1 O VAL D 50 N TYR D 32 SHEET 1 D 8 ILE B 70 ARG B 71 0 SHEET 2 D 8 ARG B 64 TYR B 67 -1 N TYR B 67 O ILE B 70 SHEET 3 D 8 ASP B 87 HIS B 92 -1 O HIS B 92 N ARG B 64 SHEET 4 D 8 ILE B 24 SER B 29 1 N SER B 29 O ALA B 91 SHEET 5 D 8 GLU B 34 ILE B 39 -1 O PHE B 37 N LEU B 26 SHEET 6 D 8 LEU D 81 TYR D 85 -1 O SER D 84 N PHE B 36 SHEET 7 D 8 ASP D 67 TYR D 78 -1 N TYR D 76 O TYR D 83 SHEET 8 D 8 SER D 88 ARG D 93 -1 O ILE D 90 N ILE D 70 SHEET 1 E 3 GLU C 9 THR C 14 0 SHEET 2 E 3 SER C 17 SER C 21 -1 O LEU C 19 N VAL C 11 SHEET 3 E 3 THR C 56 ILE C 59 -1 O ILE C 59 N LEU C 18 SHEET 1 F 3 GLU D 9 ALA D 13 0 SHEET 2 F 3 LEU D 18 SER D 21 -1 O LEU D 19 N VAL D 11 SHEET 3 F 3 THR D 56 ILE D 59 -1 O ILE D 59 N LEU D 18 CISPEP 1 ILE A 96 GLY A 97 0 -2.74 CISPEP 2 VAL C 4 PRO C 5 0 -0.68 CISPEP 3 SER D 3 VAL D 4 0 -3.76 CISPEP 4 VAL D 4 PRO D 5 0 -0.88 CISPEP 5 SER D 27 SER D 28 0 3.77 SITE 1 AC1 6 GLU A 21 HIS A 23 ASN A 25 LYS A 38 SITE 2 AC1 6 ASP A 85 GLU C 47 SITE 1 AC2 5 SER A 32 SER A 33 GLU A 34 HOH A 107 SITE 2 AC2 5 SER C 86 SITE 1 AC3 6 TYR A 67 ASP A 68 ASP A 87 ILE A 88 SITE 2 AC3 6 SER C 25 HOH C 118 SITE 1 AC4 3 ASP A 68 ILE A 70 THR D 49 SITE 1 AC5 5 ASP A 75 HOH A 116 HOH A 117 TYR D 78 SITE 2 AC5 5 TYR D 79 SITE 1 AC6 5 ASP B 75 GLY C 41 TYR C 78 TYR C 79 SITE 2 AC6 5 HOH C 100 SITE 1 AC7 9 HOH A 109 PRO C 5 THR C 6 ASP C 23 SITE 2 AC7 9 ALA C 24 SER C 25 SER C 26 TYR C 32 SITE 3 AC7 9 HOH C 116 SITE 1 AC8 3 ASN C 91 TYR C 92 ARG C 93 CRYST1 59.637 175.462 52.830 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 0.016768 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005699 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018929 0.00000