HEADER PROTEIN TRANSPORT 07-JAN-09 2ZXT TITLE CRYSTAL STRUCTURE OF TIM40/MIA40, A DISULFIDE RELAY SYSTEM IN TITLE 2 MITOCHONDRIA, SOLVED AS MBP FUSION PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: MALTOSE-BINDING PERIPLASMIC PROTEIN, LINKER, MITOCHONDRIAL COMPND 3 INTERMEMBRANE SPACE IMPORT AND ASSEMBLY PROTEIN 40; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: MBPTIM40C4; COMPND 6 SYNONYM: MMBP, MALTODEXTRIN-BINDING PROTEIN, MITOCHONDRIAL IMPORT COMPND 7 INNER MEMBRANE TRANSLOCASE TIM40; COMPND 8 ENGINEERED: YES; COMPND 9 OTHER_DETAILS: THE FUSION PROTEIN OF MMBP (UNP RESIDUES 27-392), COMPND 10 LINKER (NSSSVPGRGSIEGRPEF), MITOCHONDRIAL IMPORT INNER MEMBRANE COMPND 11 TRANSLOCASE TIM40 (UNP RESIDUES 284-365) SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI (STRAIN K12), SYNTHETIC SOURCE 3 CONSTRUCT, SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / S288C); SOURCE 4 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 5 ORGANISM_TAXID: 83333, 32630, 559292; SOURCE 6 ORGANELLE: MITOCHONDRIA; SOURCE 7 GENE: MIA40, TIM40, YKL195W; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: ROSETTA (DE3); SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PMAL-C2 KEYWDS DISULFIDE BOND, ALPHA HELIX, FUSION, SUGAR TRANSPORT, TRANSPORT, KEYWDS 2 MEMBRANE, MITOCHONDRION, MITOCHONDRION INNER MEMBRANE, KEYWDS 3 PHOSPHOPROTEIN, PROTEIN TRANSPORT, SIGNAL-ANCHOR, TRANSIT PEPTIDE, KEYWDS 4 TRANSLOCATION, TRANSMEMBRANE EXPDTA X-RAY DIFFRACTION AUTHOR S.KAWANO,T.MOMOSE,N.WATANABE,T.ENDO REVDAT 6 01-NOV-23 2ZXT 1 HETSYN REVDAT 5 29-JUL-20 2ZXT 1 COMPND REMARK HET HETNAM REVDAT 5 2 1 FORMUL LINK SITE ATOM REVDAT 4 28-JUN-17 2ZXT 1 SOURCE REVDAT 3 16-JUL-14 2ZXT 1 JRNL REVDAT 2 13-JUL-11 2ZXT 1 VERSN REVDAT 1 04-AUG-09 2ZXT 0 JRNL AUTH S.KAWANO,K.YAMANO,M.NAOE,T.MOMOSE,K.TERAO,S.NISHIKAWA, JRNL AUTH 2 N.WATANABE,T.ENDO JRNL TITL STRUCTURAL BASIS OF YEAST TIM40/MIA40 AS AN OXIDATIVE JRNL TITL 2 TRANSLOCATOR IN THE MITOCHONDRIAL INTERMEMBRANE SPACE. JRNL REF PROC.NATL.ACAD.SCI.USA V. 106 14403 2009 JRNL REFN ISSN 0027-8424 JRNL PMID 19667201 JRNL DOI 10.1073/PNAS.0901793106 REMARK 2 REMARK 2 RESOLUTION. 3.00 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) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.33 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 9184 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) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.278 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 464 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) : 3.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.08 REMARK 3 REFLECTION IN BIN (WORKING SET) : 654 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.56 REMARK 3 BIN R VALUE (WORKING SET) : 0.3240 REMARK 3 BIN FREE R VALUE SET COUNT : 31 REMARK 3 BIN FREE R VALUE : 0.4630 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3506 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 23 REMARK 3 SOLVENT ATOMS : 23 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 22.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 8.36 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.81000 REMARK 3 B22 (A**2) : 0.19000 REMARK 3 B33 (A**2) : 0.62000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.529 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.429 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 50.493 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.918 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.870 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3626 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4922 ; 1.241 ; 1.967 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 450 ; 5.853 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 164 ;39.537 ;25.671 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 593 ;20.088 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;16.701 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 522 ; 0.083 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2785 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1806 ; 0.213 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2501 ; 0.310 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 102 ; 0.145 ; 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): 26 ; 0.292 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 2 ; 0.036 ; 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): 2282 ; 0.342 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3595 ; 0.623 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1524 ; 0.773 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1327 ; 1.338 ; 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 3 A 453 REMARK 3 ORIGIN FOR THE GROUP (A): -18.1880 -2.0610 -19.0940 REMARK 3 T TENSOR REMARK 3 T11: 0.4560 T22: -0.0233 REMARK 3 T33: 0.0818 T12: 0.0971 REMARK 3 T13: -0.0093 T23: -0.0128 REMARK 3 L TENSOR REMARK 3 L11: 0.4321 L22: 1.6371 REMARK 3 L33: 2.9354 L12: 0.6062 REMARK 3 L13: -0.3257 L23: -1.2673 REMARK 3 S TENSOR REMARK 3 S11: 0.0194 S12: 0.0328 S13: 0.0695 REMARK 3 S21: 0.0699 S22: -0.0289 S23: 0.0897 REMARK 3 S31: -0.5562 S32: -0.0685 S33: 0.0094 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 2ZXT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-JAN-09. REMARK 100 THE DEPOSITION ID IS D_1000028560. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-SEP-08 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E+ SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS VII REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9692 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 90.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 12.60 REMARK 200 R MERGE (I) : 0.09200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.60 REMARK 200 R MERGE FOR SHELL (I) : 0.30900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 22.20 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 ENTRY 1ANF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM KOAC, 200 MM NH4OAC, 30 % PEG REMARK 280 4000, PH 5.6, VAPOR DIFFUSION, SITTING 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 20.63150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.67750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 50.70150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.67750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.63150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 50.70150 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, 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 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 LYS A 1 REMARK 465 ILE A 2 REMARK 465 GLU A 454 REMARK 465 THR A 455 REMARK 465 SER A 456 REMARK 465 ASP A 457 REMARK 465 ASP A 458 REMARK 465 GLU A 459 REMARK 465 GLU A 460 REMARK 465 PRO A 461 REMARK 465 GLN A 462 REMARK 465 ASP A 463 REMARK 465 LYS A 464 REMARK 465 VAL A 465 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 LEU A 113 CA - CB - CG ANGL. DEV. = 14.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLN A 49 -73.12 -69.42 REMARK 500 THR A 53 41.39 -103.46 REMARK 500 ASN A 100 62.39 60.60 REMARK 500 TYR A 117 175.56 -35.30 REMARK 500 ASP A 120 -33.40 81.07 REMARK 500 GLU A 130 -14.80 -47.53 REMARK 500 ALA A 141 -24.48 -159.93 REMARK 500 LYS A 142 -129.98 -107.36 REMARK 500 LYS A 144 37.83 -80.68 REMARK 500 ALA A 168 -90.89 -80.09 REMARK 500 ASP A 207 68.26 -105.83 REMARK 500 ASN A 241 77.55 -68.09 REMARK 500 ALA A 269 42.89 -103.86 REMARK 500 ASN A 272 70.76 -112.20 REMARK 500 TYR A 283 -44.10 -134.64 REMARK 500 LEU A 285 44.62 -77.80 REMARK 500 ASP A 296 -70.90 -71.69 REMARK 500 ASP A 314 108.77 -46.62 REMARK 500 ARG A 354 -32.23 -36.25 REMARK 500 GLU A 382 -18.52 -49.73 REMARK 500 PRO A 387 9.98 -67.53 REMARK 500 TYR A 448 79.40 -103.60 REMARK 500 ALA A 449 44.39 -72.62 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 TYR A 117 ASN A 118 147.62 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3A3C RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE FUSION PROTEIN OF MMBP (UNP RESIDUES 27-392), LINKER REMARK 999 (NSSSVPGRGSIEGRPEF), MITOCHONDRIAL IMPORT INNER MEMBRANE REMARK 999 TRANSLOCASE TIM40 (UNP RESIDUES 284-365) DBREF 2ZXT A 1 366 UNP P0AEX9 MALE_ECOLI 27 392 DBREF 2ZXT A 367 383 PDB 2ZXT 2ZXT 367 383 DBREF 2ZXT A 384 465 UNP P36046 MIA40_YEAST 284 365 SEQRES 1 A 465 LYS ILE GLU GLU GLY LYS LEU VAL ILE TRP ILE ASN GLY SEQRES 2 A 465 ASP LYS GLY TYR ASN GLY LEU ALA GLU VAL GLY LYS LYS SEQRES 3 A 465 PHE GLU LYS ASP THR GLY ILE LYS VAL THR VAL GLU HIS SEQRES 4 A 465 PRO ASP LYS LEU GLU GLU LYS PHE PRO GLN VAL ALA ALA SEQRES 5 A 465 THR GLY ASP GLY PRO ASP ILE ILE PHE TRP ALA HIS ASP SEQRES 6 A 465 ARG PHE GLY GLY TYR ALA GLN SER GLY LEU LEU ALA GLU SEQRES 7 A 465 ILE THR PRO ASP LYS ALA PHE GLN ASP LYS LEU TYR PRO SEQRES 8 A 465 PHE THR TRP ASP ALA VAL ARG TYR ASN GLY LYS LEU ILE SEQRES 9 A 465 ALA TYR PRO ILE ALA VAL GLU ALA LEU SER LEU ILE TYR SEQRES 10 A 465 ASN LYS ASP LEU LEU PRO ASN PRO PRO LYS THR TRP GLU SEQRES 11 A 465 GLU ILE PRO ALA LEU ASP LYS GLU LEU LYS ALA LYS GLY SEQRES 12 A 465 LYS SER ALA LEU MET PHE ASN LEU GLN GLU PRO TYR PHE SEQRES 13 A 465 THR TRP PRO LEU ILE ALA ALA ASP GLY GLY TYR ALA PHE SEQRES 14 A 465 LYS TYR GLU ASN GLY LYS TYR ASP ILE LYS ASP VAL GLY SEQRES 15 A 465 VAL ASP ASN ALA GLY ALA LYS ALA GLY LEU THR PHE LEU SEQRES 16 A 465 VAL ASP LEU ILE LYS ASN LYS HIS MET ASN ALA ASP THR SEQRES 17 A 465 ASP TYR SER ILE ALA GLU ALA ALA PHE ASN LYS GLY GLU SEQRES 18 A 465 THR ALA MET THR ILE ASN GLY PRO TRP ALA TRP SER ASN SEQRES 19 A 465 ILE ASP THR SER LYS VAL ASN TYR GLY VAL THR VAL LEU SEQRES 20 A 465 PRO THR PHE LYS GLY GLN PRO SER LYS PRO PHE VAL GLY SEQRES 21 A 465 VAL LEU SER ALA GLY ILE ASN ALA ALA SER PRO ASN LYS SEQRES 22 A 465 GLU LEU ALA LYS GLU PHE LEU GLU ASN TYR LEU LEU THR SEQRES 23 A 465 ASP GLU GLY LEU GLU ALA VAL ASN LYS ASP LYS PRO LEU SEQRES 24 A 465 GLY ALA VAL ALA LEU LYS SER TYR GLU GLU GLU LEU ALA SEQRES 25 A 465 LYS ASP PRO ARG ILE ALA ALA THR MET GLU ASN ALA GLN SEQRES 26 A 465 LYS GLY GLU ILE MET PRO ASN ILE PRO GLN MET SER ALA SEQRES 27 A 465 PHE TRP TYR ALA VAL ARG THR ALA VAL ILE ASN ALA ALA SEQRES 28 A 465 SER GLY ARG GLN THR VAL ASP GLU ALA LEU LYS ASP ALA SEQRES 29 A 465 GLN THR ASN SER SER SER VAL PRO GLY ARG GLY SER ILE SEQRES 30 A 465 GLU GLY ARG PRO GLU PHE ALA TYR ASN PRO ASP THR GLY SEQRES 31 A 465 GLU ILE ASN TRP ASP CYS PRO CYS LEU GLY GLY MET ALA SEQRES 32 A 465 HIS GLY PRO CYS GLY GLU GLU PHE LYS SER ALA PHE SER SEQRES 33 A 465 CYS PHE VAL TYR SER GLU ALA GLU PRO LYS GLY ILE ASP SEQRES 34 A 465 CYS VAL GLU LYS PHE GLN HIS MET GLN ASP CYS PHE ARG SEQRES 35 A 465 LYS TYR PRO GLU HIS TYR ALA GLU GLN LEU LYS GLU THR SEQRES 36 A 465 SER ASP ASP GLU GLU PRO GLN ASP LYS VAL HET GLC B 1 12 HET GLC B 2 11 HETNAM GLC ALPHA-D-GLUCOPYRANOSE HETSYN GLC ALPHA-D-GLUCOSE; D-GLUCOSE; GLUCOSE FORMUL 2 GLC 2(C6 H12 O6) FORMUL 3 HOH *23(H2 O) HELIX 1 1 GLY A 16 GLY A 32 1 17 HELIX 2 2 LYS A 42 THR A 53 1 12 HELIX 3 3 ARG A 66 SER A 73 1 8 HELIX 4 4 ASP A 82 ASP A 87 1 6 HELIX 5 5 TYR A 90 ALA A 96 1 7 HELIX 6 6 ILE A 132 LYS A 137 1 6 HELIX 7 7 GLU A 153 ASP A 164 1 12 HELIX 8 8 ASN A 185 ASN A 201 1 17 HELIX 9 9 ASP A 209 GLY A 220 1 12 HELIX 10 10 ALA A 231 LYS A 239 1 9 HELIX 11 11 THR A 249 GLN A 253 5 5 HELIX 12 12 ASN A 272 TYR A 283 1 12 HELIX 13 13 THR A 286 LYS A 297 1 12 HELIX 14 14 LEU A 304 GLU A 309 1 6 HELIX 15 15 GLU A 310 ALA A 312 5 3 HELIX 16 16 ASP A 314 GLY A 327 1 14 HELIX 17 17 GLN A 335 SER A 352 1 18 HELIX 18 18 THR A 356 SER A 369 1 14 HELIX 19 19 ARG A 380 PHE A 383 5 4 HELIX 20 20 CYS A 396 GLY A 400 5 5 HELIX 21 21 CYS A 407 SER A 421 1 15 HELIX 22 22 GLY A 427 ASP A 429 5 3 HELIX 23 23 CYS A 430 ARG A 442 1 13 SHEET 1 A 6 VAL A 35 GLU A 38 0 SHEET 2 A 6 LEU A 7 TRP A 10 1 N LEU A 7 O THR A 36 SHEET 3 A 6 ILE A 59 ALA A 63 1 O PHE A 61 N TRP A 10 SHEET 4 A 6 PHE A 258 ILE A 266 -1 O GLY A 265 N ILE A 60 SHEET 5 A 6 TYR A 106 GLU A 111 -1 N ILE A 108 O LEU A 262 SHEET 6 A 6 ALA A 301 VAL A 302 -1 O ALA A 301 N VAL A 110 SHEET 1 B 5 VAL A 35 GLU A 38 0 SHEET 2 B 5 LEU A 7 TRP A 10 1 N LEU A 7 O THR A 36 SHEET 3 B 5 ILE A 59 ALA A 63 1 O PHE A 61 N TRP A 10 SHEET 4 B 5 PHE A 258 ILE A 266 -1 O GLY A 265 N ILE A 60 SHEET 5 B 5 GLU A 328 ILE A 329 1 O GLU A 328 N VAL A 259 SHEET 1 C 3 THR A 225 ASN A 227 0 SHEET 2 C 3 SER A 114 ILE A 116 -1 N ILE A 116 O THR A 225 SHEET 3 C 3 VAL A 244 THR A 245 -1 O THR A 245 N LEU A 115 SHEET 1 D 2 TYR A 167 GLU A 172 0 SHEET 2 D 2 LYS A 175 GLY A 182 -1 O GLY A 182 N TYR A 167 SHEET 1 E 2 TYR A 385 ASN A 386 0 SHEET 2 E 2 GLU A 391 ILE A 392 -1 O GLU A 391 N ASN A 386 SSBOND 1 CYS A 396 CYS A 398 1555 1555 2.07 SSBOND 2 CYS A 407 CYS A 440 1555 1555 2.04 SSBOND 3 CYS A 417 CYS A 430 1555 1555 2.05 LINK O4 GLC B 1 C1 GLC B 2 1555 1555 1.42 CISPEP 1 GLU A 424 PRO A 425 0 1.77 CRYST1 41.263 101.403 109.355 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 0.024235 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009862 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009145 0.00000