HEADER TRANSPORT PROTEIN 05-MAY-16 5JQO OBSLTE 02-OCT-19 5JQO 6KYL TITLE CRYSTAL STRUCTURE OF PHOSPHATIDIC ACID TRANSPORTER UPS1/MDM35 IN TITLE 2 COMPLEX WITH (2R)-3-(PHOSPHONOOXY)PROPANE-1,2-DIYL DIHEXANOATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: MITOCHONDRIAL DISTRIBUTION AND MORPHOLOGY PROTEIN 35; COMPND 3 CHAIN: A, C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: PROTEIN UPS1, MITOCHONDRIAL; COMPND 7 CHAIN: B, D; COMPND 8 SYNONYM: UNPROCESSED MGM1 PROTEIN 1; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE S288C; SOURCE 3 ORGANISM_COMMON: YEAST; SOURCE 4 ORGANISM_TAXID: 559292; SOURCE 5 STRAIN: S288C; SOURCE 6 GENE: MDM35, YKL053C-A; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE S288C; SOURCE 12 ORGANISM_COMMON: YEAST; SOURCE 13 ORGANISM_TAXID: 559292; SOURCE 14 STRAIN: S288C; SOURCE 15 GENE: UPS1, YLR193C; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS LIPID TRANSPORT, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.LU,K.C.CHAN,Y.ZHAI,J.FAN,F.SUN REVDAT 2 02-OCT-19 5JQO 1 OBSLTE REVDAT 1 12-JUL-17 5JQO 0 JRNL AUTH J.LU,K.C.CHAN,Y.ZHAI,J.FAN,F.SUN JRNL TITL STRUCTURE OF A PHOSPHOLIPID TRANSPORT COMPLEX JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8_1069 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.07 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 7750 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.288 REMARK 3 R VALUE (WORKING SET) : 0.286 REMARK 3 FREE R VALUE : 0.327 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 389 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 45.0736 - 5.1169 1.00 2559 136 0.2941 0.3033 REMARK 3 2 5.1169 - 4.0622 1.00 2507 127 0.2628 0.3213 REMARK 3 3 4.0622 - 3.5490 0.91 2295 126 0.3046 0.3605 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.630 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.540 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 63.34 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.013 3395 REMARK 3 ANGLE : 1.784 4603 REMARK 3 CHIRALITY : 0.086 528 REMARK 3 PLANARITY : 0.010 572 REMARK 3 DIHEDRAL : 14.492 1191 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -0.6352 45.9878 -9.4494 REMARK 3 T TENSOR REMARK 3 T11: 0.4627 T22: 0.4305 REMARK 3 T33: 0.5186 T12: -0.1690 REMARK 3 T13: -0.0581 T23: -0.0821 REMARK 3 L TENSOR REMARK 3 L11: 1.0502 L22: 0.9956 REMARK 3 L33: 1.8007 L12: 1.0911 REMARK 3 L13: -1.3794 L23: -1.3622 REMARK 3 S TENSOR REMARK 3 S11: -0.0267 S12: -0.0840 S13: 0.0043 REMARK 3 S21: -0.0538 S22: 0.0174 S23: 0.0497 REMARK 3 S31: 0.0162 S32: 0.0335 S33: -0.0018 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5JQO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-MAY-16. REMARK 100 THE DEPOSITION ID IS D_1000221023. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JUL-15 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 : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9786 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER PLATINUM 135 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8015 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.550 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 0.67000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.8_1069 REMARK 200 STARTING MODEL: 5JQL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30%-32% V/V TACSCIMATE,PH7.0, 0.1M BIS REMARK 280 -TRIS PROPANE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 40.65950 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 20.32975 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 60.98925 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: 1560 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 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: 1570 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 MET A 1 REMARK 465 GLY A 2 REMARK 465 ASN A 3 REMARK 465 ILE A 4 REMARK 465 MET A 5 REMARK 465 LYS A 34 REMARK 465 GLY A 35 REMARK 465 LYS A 36 REMARK 465 SER A 37 REMARK 465 VAL A 38 REMARK 465 GLU A 39 REMARK 465 PHE A 75 REMARK 465 GLU A 76 REMARK 465 ASN A 77 REMARK 465 GLY A 78 REMARK 465 GLY A 79 REMARK 465 LYS A 80 REMARK 465 LEU A 81 REMARK 465 LYS A 82 REMARK 465 GLU A 83 REMARK 465 VAL A 84 REMARK 465 ASP A 85 REMARK 465 LYS A 86 REMARK 465 MET B -13 REMARK 465 GLY B -12 REMARK 465 SER B -11 REMARK 465 SER B -10 REMARK 465 HIS B -9 REMARK 465 HIS B -8 REMARK 465 HIS B -7 REMARK 465 HIS B -6 REMARK 465 HIS B -5 REMARK 465 HIS B -4 REMARK 465 SER B -3 REMARK 465 GLN B -2 REMARK 465 ASP B -1 REMARK 465 LEU B 62 REMARK 465 PRO B 63 REMARK 465 THR B 64 REMARK 465 TRP B 65 REMARK 465 VAL B 66 REMARK 465 LYS B 67 REMARK 465 PRO B 68 REMARK 465 PHE B 69 REMARK 465 LEU B 70 REMARK 465 ARG B 71 REMARK 465 GLY B 72 REMARK 465 ILE B 73 REMARK 465 ASP B 115 REMARK 465 LEU B 167 REMARK 465 GLU B 168 REMARK 465 GLU B 169 REMARK 465 ALA B 170 REMARK 465 ARG B 171 REMARK 465 ASN B 172 REMARK 465 PRO B 173 REMARK 465 GLN B 174 REMARK 465 PHE B 175 REMARK 465 MET C 1 REMARK 465 GLY C 2 REMARK 465 ASN C 3 REMARK 465 ILE C 4 REMARK 465 LEU C 33 REMARK 465 LYS C 34 REMARK 465 GLY C 35 REMARK 465 LYS C 36 REMARK 465 SER C 37 REMARK 465 VAL C 38 REMARK 465 GLU C 39 REMARK 465 PHE C 75 REMARK 465 GLU C 76 REMARK 465 ASN C 77 REMARK 465 GLY C 78 REMARK 465 GLY C 79 REMARK 465 LYS C 80 REMARK 465 LEU C 81 REMARK 465 LYS C 82 REMARK 465 GLU C 83 REMARK 465 VAL C 84 REMARK 465 ASP C 85 REMARK 465 LYS C 86 REMARK 465 MET D -13 REMARK 465 GLY D -12 REMARK 465 SER D -11 REMARK 465 SER D -10 REMARK 465 HIS D -9 REMARK 465 HIS D -8 REMARK 465 HIS D -7 REMARK 465 HIS D -6 REMARK 465 HIS D -5 REMARK 465 HIS D -4 REMARK 465 SER D -3 REMARK 465 GLN D -2 REMARK 465 ASP D -1 REMARK 465 VAL D 66 REMARK 465 LYS D 67 REMARK 465 PRO D 68 REMARK 465 PHE D 69 REMARK 465 LEU D 70 REMARK 465 ARG D 71 REMARK 465 GLY D 72 REMARK 465 LEU D 167 REMARK 465 GLU D 168 REMARK 465 GLU D 169 REMARK 465 ALA D 170 REMARK 465 ARG D 171 REMARK 465 ASN D 172 REMARK 465 PRO D 173 REMARK 465 GLN D 174 REMARK 465 PHE D 175 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 GLU A 26 CG CD OE1 OE2 REMARK 470 GLU A 30 CG CD OE1 OE2 REMARK 470 LYS A 31 CG CD CE NZ REMARK 470 LEU A 33 CG CD1 CD2 REMARK 470 ASN A 40 CG OD1 ND2 REMARK 470 LYS A 44 CG CD CE NZ REMARK 470 LYS A 59 CG CD CE NZ REMARK 470 GLN A 60 CG CD OE1 NE2 REMARK 470 GLU A 72 CG CD OE1 OE2 REMARK 470 PRO B 0 CG CD REMARK 470 LYS B 6 CG CD CE NZ REMARK 470 ASP B 14 CG OD1 OD2 REMARK 470 PHE B 15 CG CD1 CD2 CE1 CE2 CZ REMARK 470 VAL B 18 CG1 CG2 REMARK 470 VAL B 44 CG1 CG2 REMARK 470 ASP B 45 CG OD1 OD2 REMARK 470 GLN B 46 CG CD OE1 NE2 REMARK 470 GLU B 47 CG CD OE1 OE2 REMARK 470 LYS B 61 CG CD CE NZ REMARK 470 THR B 74 OG1 CG2 REMARK 470 GLN B 113 CG CD OE1 NE2 REMARK 470 PHE B 114 CG CD1 CD2 CE1 CE2 CZ REMARK 470 SER B 116 OG REMARK 470 THR B 121 OG1 CG2 REMARK 470 ARG B 126 CG CD NE CZ NH1 NH2 REMARK 470 PHE B 133 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASN B 134 CG OD1 ND2 REMARK 470 MET B 135 CG SD CE REMARK 470 ASP B 143 CG OD1 OD2 REMARK 470 ARG B 146 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 155 CG CD CE NZ REMARK 470 ARG B 157 CG CD NE CZ NH1 NH2 REMARK 470 LYS C 19 CG CD CE NZ REMARK 470 GLU C 26 CG CD OE1 OE2 REMARK 470 GLU C 30 CG CD OE1 OE2 REMARK 470 LYS C 31 CG CD CE NZ REMARK 470 ASN C 40 CG OD1 ND2 REMARK 470 GLU C 41 CG CD OE1 OE2 REMARK 470 LYS C 59 CG CD CE NZ REMARK 470 GLN C 60 CG CD OE1 NE2 REMARK 470 GLU C 68 CG CD OE1 OE2 REMARK 470 GLU C 72 CG CD OE1 OE2 REMARK 470 PRO D 0 CG CD REMARK 470 LEU D 4 CG CD1 CD2 REMARK 470 LYS D 6 CG CD CE NZ REMARK 470 ASP D 14 CG OD1 OD2 REMARK 470 PHE D 15 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASP D 45 CG OD1 OD2 REMARK 470 LYS D 61 CG CD CE NZ REMARK 470 LEU D 62 CG CD1 CD2 REMARK 470 THR D 64 OG1 CG2 REMARK 470 TRP D 65 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP D 65 CZ3 CH2 REMARK 470 ILE D 73 CG1 CG2 CD1 REMARK 470 GLU D 75 CG CD OE1 OE2 REMARK 470 ASN D 88 CG OD1 ND2 REMARK 470 GLN D 113 CG CD OE1 NE2 REMARK 470 PHE D 114 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASP D 115 CG OD1 OD2 REMARK 470 SER D 116 OG REMARK 470 PHE D 133 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASN D 134 CG OD1 ND2 REMARK 470 MET D 135 CG SD CE REMARK 470 ILE D 137 CG1 CG2 CD1 REMARK 470 LYS D 140 CG CD CE NZ REMARK 470 ARG D 146 CG CD NE CZ NH1 NH2 REMARK 470 ARG D 157 CG 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 ARG A 70 CB GLU A 72 1.83 REMARK 500 OG SER C 6 O TYR D 26 2.11 REMARK 500 OH TYR A 49 OD1 ASP B 38 2.12 REMARK 500 SG CYS C 23 CB CYS C 42 2.15 REMARK 500 OD1 ASP C 67 NH1 ARG C 70 2.15 REMARK 500 OG SER A 6 O TYR B 26 2.17 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 OH TYR A 47 OH TYR C 47 2564 1.84 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 PRO C 11 C - N - CA ANGL. DEV. = -10.2 DEGREES REMARK 500 PRO D 63 C - N - CD ANGL. DEV. = 13.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLU A 72 98.05 91.58 REMARK 500 GLU C 72 117.96 118.22 REMARK 500 SER D 131 -78.28 -101.04 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 GLU C 71 GLU C 72 -38.78 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 TYR B 30 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 LYS A 59 -10.64 REMARK 500 GLN A 60 -14.66 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 44E B 201 REMARK 610 44E D 201 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 44E B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 44E D 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide CYS C 23 and CYS C REMARK 800 42 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5JQL RELATED DB: PDB REMARK 900 RELATED ID: 5JQM RELATED DB: PDB DBREF 5JQO A 1 86 UNP O60200 MDM35_YEAST 1 86 DBREF 5JQO B 1 175 UNP Q05776 UPS1_YEAST 1 175 DBREF 5JQO C 1 86 UNP O60200 MDM35_YEAST 1 86 DBREF 5JQO D 1 175 UNP Q05776 UPS1_YEAST 1 175 SEQADV 5JQO MET B -13 UNP Q05776 EXPRESSION TAG SEQADV 5JQO GLY B -12 UNP Q05776 EXPRESSION TAG SEQADV 5JQO SER B -11 UNP Q05776 EXPRESSION TAG SEQADV 5JQO SER B -10 UNP Q05776 EXPRESSION TAG SEQADV 5JQO HIS B -9 UNP Q05776 EXPRESSION TAG SEQADV 5JQO HIS B -8 UNP Q05776 EXPRESSION TAG SEQADV 5JQO HIS B -7 UNP Q05776 EXPRESSION TAG SEQADV 5JQO HIS B -6 UNP Q05776 EXPRESSION TAG SEQADV 5JQO HIS B -5 UNP Q05776 EXPRESSION TAG SEQADV 5JQO HIS B -4 UNP Q05776 EXPRESSION TAG SEQADV 5JQO SER B -3 UNP Q05776 EXPRESSION TAG SEQADV 5JQO GLN B -2 UNP Q05776 EXPRESSION TAG SEQADV 5JQO ASP B -1 UNP Q05776 EXPRESSION TAG SEQADV 5JQO PRO B 0 UNP Q05776 EXPRESSION TAG SEQADV 5JQO MET D -13 UNP Q05776 EXPRESSION TAG SEQADV 5JQO GLY D -12 UNP Q05776 EXPRESSION TAG SEQADV 5JQO SER D -11 UNP Q05776 EXPRESSION TAG SEQADV 5JQO SER D -10 UNP Q05776 EXPRESSION TAG SEQADV 5JQO HIS D -9 UNP Q05776 EXPRESSION TAG SEQADV 5JQO HIS D -8 UNP Q05776 EXPRESSION TAG SEQADV 5JQO HIS D -7 UNP Q05776 EXPRESSION TAG SEQADV 5JQO HIS D -6 UNP Q05776 EXPRESSION TAG SEQADV 5JQO HIS D -5 UNP Q05776 EXPRESSION TAG SEQADV 5JQO HIS D -4 UNP Q05776 EXPRESSION TAG SEQADV 5JQO SER D -3 UNP Q05776 EXPRESSION TAG SEQADV 5JQO GLN D -2 UNP Q05776 EXPRESSION TAG SEQADV 5JQO ASP D -1 UNP Q05776 EXPRESSION TAG SEQADV 5JQO PRO D 0 UNP Q05776 EXPRESSION TAG SEQRES 1 A 86 MET GLY ASN ILE MET SER ALA SER PHE ALA PRO GLU CYS SEQRES 2 A 86 THR ASP LEU LYS THR LYS TYR ASP SER CYS PHE ASN GLU SEQRES 3 A 86 TRP TYR SER GLU LYS PHE LEU LYS GLY LYS SER VAL GLU SEQRES 4 A 86 ASN GLU CYS SER LYS GLN TRP TYR ALA TYR THR THR CYS SEQRES 5 A 86 VAL ASN ALA ALA LEU VAL LYS GLN GLY ILE LYS PRO ALA SEQRES 6 A 86 LEU ASP GLU ALA ARG GLU GLU ALA PRO PHE GLU ASN GLY SEQRES 7 A 86 GLY LYS LEU LYS GLU VAL ASP LYS SEQRES 1 B 189 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER GLN ASP SEQRES 2 B 189 PRO MET VAL LEU LEU HIS LYS SER THR HIS ILE PHE PRO SEQRES 3 B 189 THR ASP PHE ALA SER VAL SER ARG ALA PHE PHE ASN ARG SEQRES 4 B 189 TYR PRO ASN PRO TYR SER PRO HIS VAL LEU SER ILE ASP SEQRES 5 B 189 THR ILE SER ARG ASN VAL ASP GLN GLU GLY ASN LEU ARG SEQRES 6 B 189 THR THR ARG LEU LEU LYS LYS SER GLY LYS LEU PRO THR SEQRES 7 B 189 TRP VAL LYS PRO PHE LEU ARG GLY ILE THR GLU THR TRP SEQRES 8 B 189 ILE ILE GLU VAL SER VAL VAL ASN PRO ALA ASN SER THR SEQRES 9 B 189 MET LYS THR TYR THR ARG ASN LEU ASP HIS THR GLY ILE SEQRES 10 B 189 MET LYS VAL GLU GLU TYR THR THR TYR GLN PHE ASP SER SEQRES 11 B 189 ALA THR SER SER THR ILE ALA ASP SER ARG VAL LYS PHE SEQRES 12 B 189 SER SER GLY PHE ASN MET GLY ILE LYS SER LYS VAL GLU SEQRES 13 B 189 ASP TRP SER ARG THR LYS PHE ASP GLU ASN VAL LYS LYS SEQRES 14 B 189 SER ARG MET GLY MET ALA PHE VAL ILE GLN LYS LEU GLU SEQRES 15 B 189 GLU ALA ARG ASN PRO GLN PHE SEQRES 1 C 86 MET GLY ASN ILE MET SER ALA SER PHE ALA PRO GLU CYS SEQRES 2 C 86 THR ASP LEU LYS THR LYS TYR ASP SER CYS PHE ASN GLU SEQRES 3 C 86 TRP TYR SER GLU LYS PHE LEU LYS GLY LYS SER VAL GLU SEQRES 4 C 86 ASN GLU CYS SER LYS GLN TRP TYR ALA TYR THR THR CYS SEQRES 5 C 86 VAL ASN ALA ALA LEU VAL LYS GLN GLY ILE LYS PRO ALA SEQRES 6 C 86 LEU ASP GLU ALA ARG GLU GLU ALA PRO PHE GLU ASN GLY SEQRES 7 C 86 GLY LYS LEU LYS GLU VAL ASP LYS SEQRES 1 D 189 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER GLN ASP SEQRES 2 D 189 PRO MET VAL LEU LEU HIS LYS SER THR HIS ILE PHE PRO SEQRES 3 D 189 THR ASP PHE ALA SER VAL SER ARG ALA PHE PHE ASN ARG SEQRES 4 D 189 TYR PRO ASN PRO TYR SER PRO HIS VAL LEU SER ILE ASP SEQRES 5 D 189 THR ILE SER ARG ASN VAL ASP GLN GLU GLY ASN LEU ARG SEQRES 6 D 189 THR THR ARG LEU LEU LYS LYS SER GLY LYS LEU PRO THR SEQRES 7 D 189 TRP VAL LYS PRO PHE LEU ARG GLY ILE THR GLU THR TRP SEQRES 8 D 189 ILE ILE GLU VAL SER VAL VAL ASN PRO ALA ASN SER THR SEQRES 9 D 189 MET LYS THR TYR THR ARG ASN LEU ASP HIS THR GLY ILE SEQRES 10 D 189 MET LYS VAL GLU GLU TYR THR THR TYR GLN PHE ASP SER SEQRES 11 D 189 ALA THR SER SER THR ILE ALA ASP SER ARG VAL LYS PHE SEQRES 12 D 189 SER SER GLY PHE ASN MET GLY ILE LYS SER LYS VAL GLU SEQRES 13 D 189 ASP TRP SER ARG THR LYS PHE ASP GLU ASN VAL LYS LYS SEQRES 14 D 189 SER ARG MET GLY MET ALA PHE VAL ILE GLN LYS LEU GLU SEQRES 15 D 189 GLU ALA ARG ASN PRO GLN PHE HET 44E B 201 22 HET 44E D 201 22 HETNAM 44E (2R)-3-(PHOSPHONOOXY)PROPANE-1,2-DIYL DIHEXANOATE FORMUL 5 44E 2(C15 H29 O8 P) HELIX 1 AA1 ALA A 10 PHE A 32 1 23 HELIX 2 AA2 CYS A 42 ARG A 70 1 29 HELIX 3 AA3 ASP B 14 ASN B 24 1 11 HELIX 4 AA4 GLY B 132 LYS B 166 1 35 HELIX 5 AA5 CYS C 13 LYS C 31 1 19 HELIX 6 AA6 SER C 43 ASP C 67 1 25 HELIX 7 AA7 ASP D 14 ASN D 24 1 11 HELIX 8 AA8 GLY D 132 LYS D 166 1 35 SHEET 1 AA1 7 MET B 1 PHE B 11 0 SHEET 2 AA1 7 THR B 121 SER B 131 -1 O ALA B 123 N HIS B 9 SHEET 3 AA1 7 LYS B 105 GLN B 113 -1 N TYR B 109 O ARG B 126 SHEET 4 AA1 7 THR B 90 ASN B 97 -1 N MET B 91 O TYR B 112 SHEET 5 AA1 7 THR B 76 ASN B 85 -1 N ASN B 85 O THR B 90 SHEET 6 AA1 7 LEU B 50 LYS B 58 -1 N LEU B 56 O ILE B 78 SHEET 7 AA1 7 VAL B 34 VAL B 44 -1 N ASP B 38 O LEU B 55 SHEET 1 AA2 7 VAL D 2 PHE D 11 0 SHEET 2 AA2 7 SER D 120 SER D 130 -1 O ALA D 123 N HIS D 9 SHEET 3 AA2 7 LYS D 105 ASP D 115 -1 N LYS D 105 O SER D 130 SHEET 4 AA2 7 THR D 90 ASN D 97 -1 N MET D 91 O TYR D 112 SHEET 5 AA2 7 GLU D 75 ASN D 85 -1 N ASN D 85 O THR D 90 SHEET 6 AA2 7 LEU D 50 SER D 59 -1 N ARG D 54 O GLU D 80 SHEET 7 AA2 7 VAL D 34 VAL D 44 -1 N ASP D 38 O LEU D 55 SSBOND 1 CYS A 13 CYS A 52 1555 1555 2.02 SSBOND 2 CYS A 23 CYS A 42 1555 1555 1.87 SSBOND 3 CYS C 13 CYS C 52 1555 1555 2.02 SSBOND 4 CYS C 23 CYS C 42 1555 1555 2.01 LINK CB CYS C 23 SG CYS C 42 1555 1555 1.73 CISPEP 1 GLU A 71 GLU A 72 0 -5.11 CISPEP 2 TYR B 26 PRO B 27 0 -0.04 CISPEP 3 TYR D 26 PRO D 27 0 -0.73 SITE 1 AC1 8 HIS B 33 LYS B 58 SER B 59 GLY B 60 SITE 2 AC1 8 THR B 76 ILE B 78 ASN B 97 MET B 104 SITE 1 AC2 7 ASN B 152 HIS D 33 LYS D 58 THR D 76 SITE 2 AC2 7 ILE D 78 ASN D 97 MET D 104 SITE 1 AC3 11 TYR C 20 ASP C 21 SER C 22 PHE C 24 SITE 2 AC3 11 ASN C 25 GLU C 26 TRP C 27 GLU C 41 SITE 3 AC3 11 SER C 43 GLN C 45 TRP C 46 CRYST1 90.140 90.140 81.319 90.00 90.00 90.00 P 41 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 0.011094 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011094 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012297 0.00000