HEADER SIGNALING PROTEIN 04-NOV-11 4A6K TITLE CRYSTAL STRUCTURE OF SLM1-PH DOMAIN IN COMPLEX WITH D-MYO-INOSITOL-4- TITLE 2 PHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE-BINDING PROTEIN SLM1; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: PH DOMAIN, RESIDUES 469-583; COMPND 5 SYNONYM: SYNTHETIC LETHAL WITH MSS4 PROTEIN 1, TORC2 EFFECTOR PROTEIN COMPND 6 SLM1; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 EXPRESSION_SYSTEM: SACCHAROMYCES CEREVISIAE; SOURCE 6 EXPRESSION_SYSTEM_COMMON: BAKER'S YEAST; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4932 KEYWDS SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.ANAND,K.MAEDA,A.C.GAVIN REVDAT 2 01-MAY-24 4A6K 1 REMARK REVDAT 1 13-JUN-12 4A6K 0 JRNL AUTH K.ANAND,K.MAEDA,A.C.GAVIN JRNL TITL STRUCTURAL ANALYSES OF SLM1-PH DOMAIN DEMONSTRATE LIGAND JRNL TITL 2 BINDING IN THE NON-CANONICAL SITE JRNL REF PLOS ONE V. 7 36526 2012 JRNL REFN ESSN 1932-6203 JRNL PMID 22574179 JRNL DOI 10.1371/JOURNAL.PONE.0036526 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.79 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 37717 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) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1986 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2611 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2830 REMARK 3 BIN FREE R VALUE SET COUNT : 138 REMARK 3 BIN FREE R VALUE : 0.3360 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3556 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 83 REMARK 3 SOLVENT ATOMS : 304 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.94 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.15000 REMARK 3 B22 (A**2) : 0.64000 REMARK 3 B33 (A**2) : -0.78000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.04000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.148 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.147 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.095 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.025 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.910 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3687 ; 0.024 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4966 ; 2.057 ; 1.963 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 428 ; 7.622 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 158 ;34.801 ;23.165 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 662 ;15.541 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;25.371 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 545 ; 0.159 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2641 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 2166 ; 1.447 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3487 ; 2.448 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1521 ; 3.540 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1479 ; 5.502 ; 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 : 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4A6K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-NOV-11. REMARK 100 THE DEPOSITION ID IS D_1290050208. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAR-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.06650 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 80522 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 200 DATA REDUNDANCY : 4.530 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.55 REMARK 200 R MERGE FOR SHELL (I) : 0.64000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.020 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: APO STRUCTURE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 35.80500 REMARK 290 SMTRY3 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21750 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -75.1 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, 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 SER A 530 REMARK 465 THR A 531 REMARK 465 SER A 532 REMARK 465 SER A 533 REMARK 465 PRO A 534 REMARK 465 ASN A 535 REMARK 465 SER A 536 REMARK 465 THR A 537 REMARK 465 GLY A 538 REMARK 465 SER A 583 REMARK 465 ASP B 464 REMARK 465 SER B 530 REMARK 465 THR B 531 REMARK 465 SER B 532 REMARK 465 SER B 533 REMARK 465 PRO B 534 REMARK 465 ASN B 535 REMARK 465 SER B 536 REMARK 465 THR B 537 REMARK 465 GLY B 538 REMARK 465 ASP C 464 REMARK 465 HIS C 465 REMARK 465 PRO C 466 REMARK 465 SER C 532 REMARK 465 SER C 533 REMARK 465 PRO C 534 REMARK 465 ASN C 535 REMARK 465 SER C 536 REMARK 465 THR C 537 REMARK 465 THR C 582 REMARK 465 SER C 583 REMARK 465 ASP D 464 REMARK 465 HIS D 465 REMARK 465 SER D 530 REMARK 465 THR D 531 REMARK 465 SER D 532 REMARK 465 SER D 533 REMARK 465 PRO D 534 REMARK 465 ASN D 535 REMARK 465 SER D 536 REMARK 465 THR D 537 REMARK 465 GLY D 538 REMARK 465 SER D 539 REMARK 465 SER D 583 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 B 548 CG CD CE NZ REMARK 470 PHE C 467 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS C 507 CG CD CE NZ REMARK 470 LYS C 577 CE NZ REMARK 470 LYS D 501 CE NZ REMARK 470 ARG D 505 CG CD NE CZ NH1 NH2 REMARK 470 ARG D 555 CZ NH1 NH2 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 ASP A 464 CG OD1 OD2 REMARK 480 HIS A 465 CG ND1 CD2 CE1 NE2 REMARK 480 ARG A 554 CD NE CZ NH1 NH2 REMARK 480 ARG B 554 CD NE CZ NH1 NH2 REMARK 480 ARG C 554 CD NE CZ NH1 NH2 REMARK 480 ARG D 554 CD NE CZ NH1 NH2 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 O HOH B 2029 O HOH B 2030 0.69 REMARK 500 OD1 ASP A 464 OE1 GLN C 549 1.66 REMARK 500 O HOH D 2043 O HOH D 2044 2.00 REMARK 500 CB LYS B 548 O HOH B 2067 2.01 REMARK 500 O ASN C 558 O42 I4D C 1583 2.02 REMARK 500 OH TYR B 485 O6 I4D B 1586 2.06 REMARK 500 O GLY B 551 CG2 VAL D 510 2.09 REMARK 500 O HOH B 2010 O HOH B 2037 2.11 REMARK 500 OE2 GLU B 469 O HOH B 2003 2.12 REMARK 500 NE ARG A 477 O HOH A 2016 2.15 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 A 2031 O HOH C 2033 1655 0.70 REMARK 500 NH2 ARG D 527 O HOH B 2023 2546 2.01 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 ASP A 464 CB ASP A 464 CG -0.141 REMARK 500 HIS A 465 CB HIS A 465 CG -0.190 REMARK 500 ARG A 505 CZ ARG A 505 NH1 0.078 REMARK 500 GLU B 524 CB GLU B 524 CG -0.122 REMARK 500 ARG C 554 CG ARG C 554 CD 0.199 REMARK 500 ARG D 554 CG ARG D 554 CD 0.238 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 HIS A 465 CB - CA - C ANGL. DEV. = -14.4 DEGREES REMARK 500 HIS A 465 CB - CG - ND1 ANGL. DEV. = -9.1 DEGREES REMARK 500 HIS A 465 N - CA - C ANGL. DEV. = 24.8 DEGREES REMARK 500 PRO A 466 C - N - CA ANGL. DEV. = -13.9 DEGREES REMARK 500 ARG A 505 NE - CZ - NH1 ANGL. DEV. = 8.0 DEGREES REMARK 500 ARG A 505 NE - CZ - NH2 ANGL. DEV. = -6.5 DEGREES REMARK 500 ASN A 550 CB - CA - C ANGL. DEV. = -15.0 DEGREES REMARK 500 GLY A 551 N - CA - C ANGL. DEV. = 21.7 DEGREES REMARK 500 ARG A 554 CB - CG - CD ANGL. DEV. = 19.7 DEGREES REMARK 500 ASN B 550 CB - CA - C ANGL. DEV. = -15.9 DEGREES REMARK 500 GLY B 551 N - CA - C ANGL. DEV. = 26.1 DEGREES REMARK 500 ILE B 552 C - N - CA ANGL. DEV. = 15.8 DEGREES REMARK 500 ILE B 552 CB - CA - C ANGL. DEV. = -18.1 DEGREES REMARK 500 ALA B 563 CB - CA - C ANGL. DEV. = -15.3 DEGREES REMARK 500 ARG C 478 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG C 554 CB - CG - CD ANGL. DEV. = 16.5 DEGREES REMARK 500 ARG D 554 CG - CD - NE ANGL. DEV. = -16.6 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 THR C 523 -67.71 -107.81 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 ASP A 464 HIS A 465 -137.99 REMARK 500 GLY A 551 ILE A 552 142.58 REMARK 500 HIS B 465 PRO B 466 -130.40 REMARK 500 GLY B 551 ILE B 552 137.09 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 HIS A 465 0.11 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B2047 DISTANCE = 6.45 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 1583 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 1584 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 1585 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 D 1583 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 1584 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 C 1582 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 D 1584 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE I4D A 1585 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE I4D B 1586 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE I4D C 1583 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4A5K RELATED DB: PDB REMARK 900 STRUCTURAL ANALYSES OF SLM1-PH DOMAIN DEMONSTRATE LIGAND BINDING IN REMARK 900 THE NON-CANONICAL SITE REMARK 900 RELATED ID: 4A6F RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SLM1-PH DOMAIN IN COMPLEX WITH PHOSPHOSERINE REMARK 900 RELATED ID: 4A6H RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SLM1-PH DOMAIN IN COMPLEX WITH INOSITOL-4- REMARK 900 PHOSPHATE DBREF 4A6K A 469 583 UNP P40485 SLM1_YEAST 469 583 DBREF 4A6K B 469 583 UNP P40485 SLM1_YEAST 469 583 DBREF 4A6K C 469 583 UNP P40485 SLM1_YEAST 469 583 DBREF 4A6K D 469 583 UNP P40485 SLM1_YEAST 469 583 SEQADV 4A6K ASP A 464 UNP P40485 EXPRESSION TAG SEQADV 4A6K HIS A 465 UNP P40485 EXPRESSION TAG SEQADV 4A6K PRO A 466 UNP P40485 EXPRESSION TAG SEQADV 4A6K PHE A 467 UNP P40485 EXPRESSION TAG SEQADV 4A6K THR A 468 UNP P40485 EXPRESSION TAG SEQADV 4A6K ASP B 464 UNP P40485 EXPRESSION TAG SEQADV 4A6K HIS B 465 UNP P40485 EXPRESSION TAG SEQADV 4A6K PRO B 466 UNP P40485 EXPRESSION TAG SEQADV 4A6K PHE B 467 UNP P40485 EXPRESSION TAG SEQADV 4A6K THR B 468 UNP P40485 EXPRESSION TAG SEQADV 4A6K ASP C 464 UNP P40485 EXPRESSION TAG SEQADV 4A6K HIS C 465 UNP P40485 EXPRESSION TAG SEQADV 4A6K PRO C 466 UNP P40485 EXPRESSION TAG SEQADV 4A6K PHE C 467 UNP P40485 EXPRESSION TAG SEQADV 4A6K THR C 468 UNP P40485 EXPRESSION TAG SEQADV 4A6K ASP D 464 UNP P40485 EXPRESSION TAG SEQADV 4A6K HIS D 465 UNP P40485 EXPRESSION TAG SEQADV 4A6K PRO D 466 UNP P40485 EXPRESSION TAG SEQADV 4A6K PHE D 467 UNP P40485 EXPRESSION TAG SEQADV 4A6K THR D 468 UNP P40485 EXPRESSION TAG SEQRES 1 A 120 ASP HIS PRO PHE THR GLU ILE LYS SER GLY PHE LEU GLU SEQRES 2 A 120 ARG ARG SER LYS PHE LEU LYS SER TYR SER LYS GLY TYR SEQRES 3 A 120 TYR VAL LEU THR PRO ASN PHE LEU HIS GLU PHE LYS THR SEQRES 4 A 120 ALA ASP ARG LYS LYS ASP LEU VAL PRO VAL MET SER LEU SEQRES 5 A 120 ALA LEU SER GLU CYS THR VAL THR GLU HIS SER ARG LYS SEQRES 6 A 120 ASN SER THR SER SER PRO ASN SER THR GLY SER ASP ALA SEQRES 7 A 120 LYS PHE VAL LEU HIS ALA LYS GLN ASN GLY ILE ILE ARG SEQRES 8 A 120 ARG GLY HIS ASN TRP VAL PHE LYS ALA ASP SER TYR GLU SEQRES 9 A 120 SER MET MET SER TRP PHE ASP ASN LEU LYS ILE LEU THR SEQRES 10 A 120 SER THR SER SEQRES 1 B 120 ASP HIS PRO PHE THR GLU ILE LYS SER GLY PHE LEU GLU SEQRES 2 B 120 ARG ARG SER LYS PHE LEU LYS SER TYR SER LYS GLY TYR SEQRES 3 B 120 TYR VAL LEU THR PRO ASN PHE LEU HIS GLU PHE LYS THR SEQRES 4 B 120 ALA ASP ARG LYS LYS ASP LEU VAL PRO VAL MET SER LEU SEQRES 5 B 120 ALA LEU SER GLU CYS THR VAL THR GLU HIS SER ARG LYS SEQRES 6 B 120 ASN SER THR SER SER PRO ASN SER THR GLY SER ASP ALA SEQRES 7 B 120 LYS PHE VAL LEU HIS ALA LYS GLN ASN GLY ILE ILE ARG SEQRES 8 B 120 ARG GLY HIS ASN TRP VAL PHE LYS ALA ASP SER TYR GLU SEQRES 9 B 120 SER MET MET SER TRP PHE ASP ASN LEU LYS ILE LEU THR SEQRES 10 B 120 SER THR SER SEQRES 1 C 120 ASP HIS PRO PHE THR GLU ILE LYS SER GLY PHE LEU GLU SEQRES 2 C 120 ARG ARG SER LYS PHE LEU LYS SER TYR SER LYS GLY TYR SEQRES 3 C 120 TYR VAL LEU THR PRO ASN PHE LEU HIS GLU PHE LYS THR SEQRES 4 C 120 ALA ASP ARG LYS LYS ASP LEU VAL PRO VAL MET SER LEU SEQRES 5 C 120 ALA LEU SER GLU CYS THR VAL THR GLU HIS SER ARG LYS SEQRES 6 C 120 ASN SER THR SER SER PRO ASN SER THR GLY SER ASP ALA SEQRES 7 C 120 LYS PHE VAL LEU HIS ALA LYS GLN ASN GLY ILE ILE ARG SEQRES 8 C 120 ARG GLY HIS ASN TRP VAL PHE LYS ALA ASP SER TYR GLU SEQRES 9 C 120 SER MET MET SER TRP PHE ASP ASN LEU LYS ILE LEU THR SEQRES 10 C 120 SER THR SER SEQRES 1 D 120 ASP HIS PRO PHE THR GLU ILE LYS SER GLY PHE LEU GLU SEQRES 2 D 120 ARG ARG SER LYS PHE LEU LYS SER TYR SER LYS GLY TYR SEQRES 3 D 120 TYR VAL LEU THR PRO ASN PHE LEU HIS GLU PHE LYS THR SEQRES 4 D 120 ALA ASP ARG LYS LYS ASP LEU VAL PRO VAL MET SER LEU SEQRES 5 D 120 ALA LEU SER GLU CYS THR VAL THR GLU HIS SER ARG LYS SEQRES 6 D 120 ASN SER THR SER SER PRO ASN SER THR GLY SER ASP ALA SEQRES 7 D 120 LYS PHE VAL LEU HIS ALA LYS GLN ASN GLY ILE ILE ARG SEQRES 8 D 120 ARG GLY HIS ASN TRP VAL PHE LYS ALA ASP SER TYR GLU SEQRES 9 D 120 SER MET MET SER TRP PHE ASP ASN LEU LYS ILE LEU THR SEQRES 10 D 120 SER THR SER HET PO4 A1583 5 HET PO4 A1584 5 HET I4D A1585 16 HET PO4 B1584 5 HET PO4 B1585 5 HET I4D B1586 16 HET PO4 C1582 5 HET I4D C1583 16 HET PO4 D1583 5 HET PO4 D1584 5 HETNAM PO4 PHOSPHATE ION HETNAM I4D D-MYO-INOSITOL-4-PHOSPHATE FORMUL 5 PO4 7(O4 P 3-) FORMUL 7 I4D 3(C6 H13 O9 P) FORMUL 15 HOH *304(H2 O) HELIX 1 1 SER A 565 THR A 580 1 16 HELIX 2 2 SER B 565 THR B 580 1 16 HELIX 3 3 SER C 565 SER C 581 1 17 HELIX 4 4 SER D 565 SER D 581 1 17 SHEET 1 AA 7 MET A 513 ALA A 516 0 SHEET 2 AA 7 PHE A 496 PHE A 500 -1 O LEU A 497 N LEU A 515 SHEET 3 AA 7 SER A 484 LEU A 492 -1 O TYR A 489 N PHE A 500 SHEET 4 AA 7 LYS A 471 SER A 479 -1 O LYS A 471 N LEU A 492 SHEET 5 AA 7 ASN A 558 LYS A 562 -1 O VAL A 560 N ARG A 478 SHEET 6 AA 7 LYS A 542 ALA A 547 -1 O PHE A 543 N PHE A 561 SHEET 7 AA 7 CYS A 520 HIS A 525 -1 O THR A 521 N HIS A 546 SHEET 1 BA 7 MET B 513 ALA B 516 0 SHEET 2 BA 7 PHE B 496 PHE B 500 -1 O LEU B 497 N LEU B 515 SHEET 3 BA 7 SER B 484 LEU B 492 -1 O TYR B 489 N PHE B 500 SHEET 4 BA 7 LYS B 471 SER B 479 -1 O LYS B 471 N LEU B 492 SHEET 5 BA 7 ASN B 558 LYS B 562 -1 O VAL B 560 N ARG B 478 SHEET 6 BA 7 LYS B 542 ALA B 547 -1 O PHE B 543 N PHE B 561 SHEET 7 BA 7 CYS B 520 HIS B 525 -1 O THR B 521 N HIS B 546 SHEET 1 CA 7 MET C 513 ALA C 516 0 SHEET 2 CA 7 PHE C 496 PHE C 500 -1 O LEU C 497 N LEU C 515 SHEET 3 CA 7 SER C 484 LEU C 492 -1 O TYR C 489 N PHE C 500 SHEET 4 CA 7 LYS C 471 SER C 479 -1 O LYS C 471 N LEU C 492 SHEET 5 CA 7 ASN C 558 LYS C 562 -1 O VAL C 560 N ARG C 478 SHEET 6 CA 7 LYS C 542 ALA C 547 -1 O PHE C 543 N PHE C 561 SHEET 7 CA 7 CYS C 520 HIS C 525 -1 O THR C 521 N HIS C 546 SHEET 1 DA 7 MET D 513 ALA D 516 0 SHEET 2 DA 7 PHE D 496 PHE D 500 -1 O LEU D 497 N LEU D 515 SHEET 3 DA 7 SER D 484 LEU D 492 -1 O TYR D 489 N PHE D 500 SHEET 4 DA 7 LYS D 471 SER D 479 -1 O LYS D 471 N LEU D 492 SHEET 5 DA 7 ASN D 558 LYS D 562 -1 O VAL D 560 N ARG D 478 SHEET 6 DA 7 LYS D 542 ALA D 547 -1 O PHE D 543 N PHE D 561 SHEET 7 DA 7 CYS D 520 HIS D 525 -1 O THR D 521 N HIS D 546 SITE 1 AC1 8 THR A 493 ASN A 495 PHE A 496 HIS A 498 SITE 2 AC1 8 THR C 493 ASN C 495 PHE C 496 HIS C 498 SITE 1 AC2 9 THR B 493 ASN B 495 PHE B 496 HIS B 498 SITE 2 AC2 9 HOH B2002 THR D 493 ASN D 495 PHE D 496 SITE 3 AC2 9 HIS D 498 SITE 1 AC3 3 LYS B 480 HIS B 557 ASN B 558 SITE 1 AC4 3 LYS D 480 HIS D 557 ASN D 558 SITE 1 AC5 3 LYS A 480 HIS A 557 ASN A 558 SITE 1 AC6 5 HIS C 525 ARG C 527 LYS C 528 TYR C 566 SITE 2 AC6 5 HOH C2070 SITE 1 AC7 3 ARG D 478 TYR D 485 LYS D 542 SITE 1 AC8 5 TYR A 485 SER A 539 LYS A 542 LYS A 562 SITE 2 AC8 5 HOH A2075 SITE 1 AC9 4 TYR B 485 SER B 539 LYS B 542 LYS B 562 SITE 1 BC1 3 LYS C 480 HIS C 557 ASN C 558 CRYST1 36.950 71.610 82.630 90.00 90.00 90.00 P 1 21 1 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 0.027064 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013965 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012102 0.00000