HEADER ENDOCYTOSIS,EXOCYTOSIS 06-MAY-14 4PHF TITLE CRYSTAL STRUCTURE OF YPT7 COVALENTLY MODIFIED WITH GDP COMPND MOL_ID: 1; COMPND 2 MOLECULE: GTP-BINDING PROTEIN YPT7; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-182; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 559292; SOURCE 5 STRAIN: S288C; SOURCE 6 GENE: YPT7, VAM4, YML001W, YM8270.02; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS YPT7, ACRYL-NUCLEOTIDES, AGDP, COVALENT, GDP, ENDOCYTOSIS, EXOCYTOSIS EXPDTA X-RAY DIFFRACTION AUTHOR S.VIEWEG,D.WIEGANDT,F.HOFMANN,D.KOCH,Y.WU,A.ITZEN,M.P.MUELLER, AUTHOR 2 R.S.GOODY REVDAT 5 27-DEC-23 4PHF 1 LINK REVDAT 4 08-JAN-20 4PHF 1 REMARK REVDAT 3 27-SEP-17 4PHF 1 REMARK REVDAT 2 31-AUG-16 4PHF 1 JRNL REVDAT 1 28-MAY-14 4PHF 0 JRNL AUTH D.WIEGANDT,S.VIEWEG,F.HOFMANN,D.KOCH,F.LI,Y.W.WU,A.ITZEN, JRNL AUTH 2 M.P.MULLER,R.S.GOODY JRNL TITL LOCKING GTPASES COVALENTLY IN THEIR FUNCTIONAL STATES. JRNL REF NAT COMMUN V. 6 7773 2015 JRNL REFN ESSN 2041-1723 JRNL PMID 26178622 JRNL DOI 10.1038/NCOMMS8773 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.65 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 11832 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) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 623 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) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 762 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2300 REMARK 3 BIN FREE R VALUE SET COUNT : 43 REMARK 3 BIN FREE R VALUE : 0.3280 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1257 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 41 REMARK 3 SOLVENT ATOMS : 60 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.88 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.90000 REMARK 3 B22 (A**2) : 4.13000 REMARK 3 B33 (A**2) : -2.23000 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): 0.181 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.165 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.110 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.460 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.922 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1328 ; 0.019 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 859 ; 0.006 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1802 ; 1.859 ; 1.978 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2114 ; 1.127 ; 3.012 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 164 ; 6.501 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 58 ;33.671 ;25.862 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 224 ;11.904 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 4 ;13.698 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 212 ; 0.155 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1453 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 251 ; 0.001 ; 0.020 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 7 A 182 REMARK 3 RESIDUE RANGE : A 201 A 202 REMARK 3 ORIGIN FOR THE GROUP (A): -17.5600 -3.1646 1.6666 REMARK 3 T TENSOR REMARK 3 T11: 0.0596 T22: 0.0121 REMARK 3 T33: 0.0765 T12: 0.0143 REMARK 3 T13: 0.0089 T23: -0.0076 REMARK 3 L TENSOR REMARK 3 L11: 0.3632 L22: 0.4244 REMARK 3 L33: 0.8137 L12: 0.2565 REMARK 3 L13: -0.0283 L23: -0.2718 REMARK 3 S TENSOR REMARK 3 S11: -0.0122 S12: 0.0198 S13: -0.0403 REMARK 3 S21: 0.0435 S22: 0.0612 S23: -0.0072 REMARK 3 S31: -0.0997 S32: -0.0483 S33: -0.0490 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 : 1.20 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 4PHF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-MAY-14. REMARK 100 THE DEPOSITION ID IS D_1000200808. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUN-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI(111) MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12456 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 40.650 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.14100 REMARK 200 FOR THE DATA SET : 12.4100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 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) : 0.54300 REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.5 M NH4NO3, 16% (W/V) PEG3350, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 24.65500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.23500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.45000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.23500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.65500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.45000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 HIS A 0 REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 SER A 3 REMARK 465 ARG A 4 REMARK 465 LYS A 5 REMARK 465 LYS A 6 REMARK 465 GLN A 36 REMARK 465 TYR A 37 REMARK 465 LYS A 38 REMARK 465 ALA A 39 REMARK 465 ALA A 66 REMARK 465 GLY A 67 REMARK 465 GLN A 68 REMARK 465 GLU A 69 REMARK 465 ARG A 70 REMARK 465 PHE A 71 REMARK 465 GLN A 72 REMARK 465 SER A 73 REMARK 465 LEU A 74 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 OE1 GLU A 49 OD2 ASP A 151 4445 2.10 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 A 26 CG HIS A 26 CD2 0.063 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 ASP A 90 CB - CG - OD1 ANGL. DEV. = 7.3 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 LYS A 127 31.51 82.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 22 OG1 REMARK 620 2 2UH A 201 O3B 93.6 REMARK 620 3 HOH A 325 O 87.9 94.4 REMARK 620 4 HOH A 326 O 85.1 176.3 82.1 REMARK 620 5 HOH A 327 O 174.1 90.8 87.8 90.3 REMARK 620 6 HOH A 328 O 90.3 92.6 172.9 90.9 93.4 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 2UH A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO3 A 203 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4PHG RELATED DB: PDB REMARK 900 RELATED ID: 4PHH RELATED DB: PDB DBREF 4PHF A 1 182 UNP P32939 YPT7_YEAST 1 182 SEQADV 4PHF GLY A -1 UNP P32939 EXPRESSION TAG SEQADV 4PHF HIS A 0 UNP P32939 EXPRESSION TAG SEQADV 4PHF CYS A 35 UNP P32939 GLN 35 ENGINEERED MUTATION SEQRES 1 A 184 GLY HIS MET SER SER ARG LYS LYS ASN ILE LEU LYS VAL SEQRES 2 A 184 ILE ILE LEU GLY ASP SER GLY VAL GLY LYS THR SER LEU SEQRES 3 A 184 MET HIS ARG TYR VAL ASN ASP LYS TYR SER CYS GLN TYR SEQRES 4 A 184 LYS ALA THR ILE GLY ALA ASP PHE LEU THR LYS GLU VAL SEQRES 5 A 184 THR VAL ASP GLY ASP LYS VAL ALA THR MET GLN VAL TRP SEQRES 6 A 184 ASP THR ALA GLY GLN GLU ARG PHE GLN SER LEU GLY VAL SEQRES 7 A 184 ALA PHE TYR ARG GLY ALA ASP CYS CYS VAL LEU VAL TYR SEQRES 8 A 184 ASP VAL THR ASN ALA SER SER PHE GLU ASN ILE LYS SER SEQRES 9 A 184 TRP ARG ASP GLU PHE LEU VAL HIS ALA ASN VAL ASN SER SEQRES 10 A 184 PRO GLU THR PHE PRO PHE VAL ILE LEU GLY ASN LYS ILE SEQRES 11 A 184 ASP ALA GLU GLU SER LYS LYS ILE VAL SER GLU LYS SER SEQRES 12 A 184 ALA GLN GLU LEU ALA LYS SER LEU GLY ASP ILE PRO LEU SEQRES 13 A 184 PHE LEU THR SER ALA LYS ASN ALA ILE ASN VAL ASP THR SEQRES 14 A 184 ALA PHE GLU GLU ILE ALA ARG SER ALA LEU GLN GLN ASN SEQRES 15 A 184 GLN ALA HET 2UH A 201 36 HET MG A 202 1 HET NO3 A 203 4 HETNAM 2UH N-[3-(PROPANOYLAMINO)PROPYL]GUANOSINE 5'-(TRIHYDROGEN HETNAM 2 2UH DIPHOSPHATE) HETNAM MG MAGNESIUM ION HETNAM NO3 NITRATE ION FORMUL 2 2UH C16 H26 N6 O12 P2 FORMUL 3 MG MG 2+ FORMUL 4 NO3 N O3 1- FORMUL 5 HOH *60(H2 O) HELIX 1 AA1 GLY A 20 ASP A 31 1 12 HELIX 2 AA2 VAL A 76 ARG A 80 1 5 HELIX 3 AA3 ASN A 93 ASN A 99 1 7 HELIX 4 AA4 ASN A 99 ASN A 112 1 14 HELIX 5 AA5 GLU A 131 LYS A 135 5 5 HELIX 6 AA6 SER A 138 LEU A 149 1 12 HELIX 7 AA7 ASN A 164 ALA A 182 1 19 SHEET 1 AA1 6 PHE A 45 VAL A 52 0 SHEET 2 AA1 6 ASP A 55 TRP A 63 -1 O ALA A 58 N VAL A 50 SHEET 3 AA1 6 ILE A 8 LEU A 14 1 N VAL A 11 O TRP A 63 SHEET 4 AA1 6 CYS A 84 ASP A 90 1 O VAL A 86 N ILE A 12 SHEET 5 AA1 6 PHE A 121 ASN A 126 1 O VAL A 122 N LEU A 87 SHEET 6 AA1 6 LEU A 154 THR A 157 1 O PHE A 155 N ILE A 123 LINK SG CYS A 35 CAA 2UH A 201 1555 1555 1.64 LINK OG1 THR A 22 MG MG A 202 1555 1555 1.96 LINK O3B 2UH A 201 MG MG A 202 1555 1555 2.01 LINK MG MG A 202 O HOH A 325 1555 1555 2.22 LINK MG MG A 202 O HOH A 326 1555 1555 2.26 LINK MG MG A 202 O HOH A 327 1555 1555 2.08 LINK MG MG A 202 O HOH A 328 1555 1555 2.03 SITE 1 AC1 18 GLY A 18 VAL A 19 GLY A 20 LYS A 21 SITE 2 AC1 18 THR A 22 SER A 23 TYR A 33 CYS A 35 SITE 3 AC1 18 ASN A 126 LYS A 127 ASP A 129 SER A 158 SITE 4 AC1 18 ALA A 159 LYS A 160 MG A 202 HOH A 327 SITE 5 AC1 18 HOH A 328 HOH A 343 SITE 1 AC2 6 THR A 22 2UH A 201 HOH A 325 HOH A 326 SITE 2 AC2 6 HOH A 327 HOH A 328 SITE 1 AC3 8 ARG A 27 LYS A 101 ALA A 162 ILE A 163 SITE 2 AC3 8 ASN A 164 VAL A 165 ASP A 166 HOH A 314 CRYST1 49.310 54.900 60.470 90.00 90.00 90.00 P 21 21 21 4 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 0.020280 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018215 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016537 0.00000