HEADER TRANSLATION 16-NOV-17 5YT0 TITLE CRYSTAL STRUCTURE OF THE COMPLEX OF ARCHAEAL RIBOSOMAL STALK PROTEIN TITLE 2 AP1 AND ARCHAEAL TRANSLATION INITIATION FACTOR AIF5B COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE TRANSLATION INITIATION FACTOR IF-2; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: ARCHAEAL RIBOSOMAL STALK PROTEIN AP1; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AEROPYRUM PERNIX K1; SOURCE 3 ORGANISM_TAXID: 272557; SOURCE 4 STRAIN: K1; SOURCE 5 GENE: INFB, APE_2374; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: AEROPYRUM PERNIX K1; SOURCE 11 ORGANISM_TAXID: 272557 KEYWDS TRANSLATION INITIATION FACTOR, RIBOSOMAL STALK PROTEIN, COMPLEX, KEYWDS 2 TRANSLATION EXPDTA X-RAY DIFFRACTION AUTHOR R.MURAKAMI,C.R.SINGH,J.MORRIS,L.TANG,I.HARMON,T.MIYOSHI,K.ITO, AUTHOR 2 K.ASANO,T.UCHIUMI REVDAT 3 27-MAR-24 5YT0 1 REMARK REVDAT 2 15-AUG-18 5YT0 1 JRNL REVDAT 1 27-JUN-18 5YT0 0 JRNL AUTH R.MURAKAMI,C.R.SINGH,J.MORRIS,L.TANG,I.HARMON,A.TAKASU, JRNL AUTH 2 T.MIYOSHI,K.ITO,K.ASANO,T.UCHIUMI JRNL TITL THE INTERACTION BETWEEN THE RIBOSOMAL STALK PROTEINS AND JRNL TITL 2 TRANSLATION INITIATION FACTOR 5B PROMOTES TRANSLATION JRNL TITL 3 INITIATION JRNL REF MOL. CELL. BIOL. V. 38 2018 JRNL REFN ESSN 1098-5549 JRNL PMID 29844065 JRNL DOI 10.1128/MCB.00067-18 REMARK 2 REMARK 2 RESOLUTION. 1.89 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.89 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.70 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 33408 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) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1758 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) : 1.89 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.94 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2323 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.99 REMARK 3 BIN R VALUE (WORKING SET) : 0.2080 REMARK 3 BIN FREE R VALUE SET COUNT : 122 REMARK 3 BIN FREE R VALUE : 0.2810 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2660 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 151 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.28 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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): 0.119 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.123 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.081 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.729 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.945 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2742 ; 0.030 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2800 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3714 ; 2.610 ; 2.012 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6430 ; 1.276 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 339 ; 6.926 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 111 ;34.456 ;22.703 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 493 ;15.768 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;23.789 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 433 ; 0.186 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2984 ; 0.015 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 572 ; 0.002 ; 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): 1365 ; 4.383 ; 3.444 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1364 ; 4.364 ; 3.443 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1698 ; 5.091 ; 5.134 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1699 ; 5.100 ; 5.135 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1377 ; 7.103 ; 4.388 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1377 ; 7.101 ; 4.387 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2015 ;10.293 ; 6.207 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3039 ;11.662 ;29.051 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2984 ;11.695 ;28.777 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 : NULL 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 5YT0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-NOV-17. REMARK 100 THE DEPOSITION ID IS D_1300005825. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-OCT-13 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A 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 : 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 : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35221 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 42.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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) : 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M CITRIC ACID, PH 6.5, 35%(W/V) REMARK 280 PEG600, VAPOR DIFFUSION, 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 27.36000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.75500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.50800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.75500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.36000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.50800 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 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 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 ALA A 2 REMARK 465 GLY A 3 REMARK 465 ASP A 4 REMARK 465 LYS A 5 REMARK 465 GLY A 6 REMARK 465 GLY A 7 REMARK 465 GLY A 8 REMARK 465 ASP A 9 REMARK 465 GLY A 10 REMARK 465 GLU A 11 REMARK 465 ARG A 12 REMARK 465 ARG A 13 REMARK 465 GLU A 45 REMARK 465 ALA A 46 REMARK 465 GLY A 47 REMARK 465 GLY A 101 REMARK 465 LEU A 296 REMARK 465 GLN A 297 REMARK 465 ASP A 298 REMARK 465 ILE A 299 REMARK 465 ARG A 300 REMARK 465 SER A 301 REMARK 465 ARG A 302 REMARK 465 GLU A 303 REMARK 465 ALA A 304 REMARK 465 ARG A 305 REMARK 465 HIS A 359 REMARK 465 HIS A 360 REMARK 465 HIS A 361 REMARK 465 HIS A 362 REMARK 465 HIS A 363 REMARK 465 HIS A 364 REMARK 465 LYS B 91 REMARK 465 LYS B 92 REMARK 465 LYS B 93 REMARK 465 LYS B 94 REMARK 465 LYS B 95 REMARK 465 LYS B 96 REMARK 465 GLU B 97 REMARK 465 GLU B 98 REMARK 465 GLU B 99 REMARK 465 VAL B 100 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 87 CG ASP A 87 OD1 0.158 REMARK 500 GLU A 191 CD GLU A 191 OE1 0.077 REMARK 500 SER A 209 CB SER A 209 OG 0.089 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 ARG A 37 NE - CZ - NH1 ANGL. DEV. = 5.3 DEGREES REMARK 500 ARG A 37 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 38 NE - CZ - NH2 ANGL. DEV. = -4.4 DEGREES REMARK 500 ASP A 87 CB - CG - OD1 ANGL. DEV. = 10.6 DEGREES REMARK 500 ASP A 87 CB - CG - OD2 ANGL. DEV. = -12.3 DEGREES REMARK 500 ARG A 99 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ASP A 113 CB - CG - OD1 ANGL. DEV. = 7.9 DEGREES REMARK 500 MET A 115 CG - SD - CE ANGL. DEV. = 17.1 DEGREES REMARK 500 ARG A 132 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 132 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 145 NE - CZ - NH2 ANGL. DEV. = -4.4 DEGREES REMARK 500 ARG A 162 NE - CZ - NH1 ANGL. DEV. = -6.0 DEGREES REMARK 500 ARG A 162 NE - CZ - NH2 ANGL. DEV. = 5.6 DEGREES REMARK 500 ARG A 169 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 175 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 211 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 ARG A 211 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ASP A 265 CB - CG - OD1 ANGL. DEV. = 7.6 DEGREES REMARK 500 ASP A 265 CB - CG - OD2 ANGL. DEV. = -6.4 DEGREES REMARK 500 ARG A 279 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 288 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 288 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 319 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ASP A 326 CB - CG - OD1 ANGL. DEV. = 7.6 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 PHE A 255 -2.62 -152.24 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GDP A 500 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5FG3 RELATED DB: PDB DBREF 5YT0 A 1 358 UNP Q9Y9B3 IF2P_AERPE 1 358 DBREF 5YT0 B 91 111 PDB 5YT0 5YT0 91 111 SEQADV 5YT0 HIS A 359 UNP Q9Y9B3 EXPRESSION TAG SEQADV 5YT0 HIS A 360 UNP Q9Y9B3 EXPRESSION TAG SEQADV 5YT0 HIS A 361 UNP Q9Y9B3 EXPRESSION TAG SEQADV 5YT0 HIS A 362 UNP Q9Y9B3 EXPRESSION TAG SEQADV 5YT0 HIS A 363 UNP Q9Y9B3 EXPRESSION TAG SEQADV 5YT0 HIS A 364 UNP Q9Y9B3 EXPRESSION TAG SEQRES 1 A 364 MET ALA GLY ASP LYS GLY GLY GLY ASP GLY GLU ARG ARG SEQRES 2 A 364 LEU ARG GLN PRO ILE VAL VAL VAL LEU GLY HIS VAL ASP SEQRES 3 A 364 HIS GLY LYS THR THR LEU LEU ASP LYS ILE ARG ARG THR SEQRES 4 A 364 ALA VAL ALA ALA LYS GLU ALA GLY GLY ILE THR GLN HIS SEQRES 5 A 364 ILE GLY ALA SER ILE VAL PRO ALA ASP VAL ILE GLU LYS SEQRES 6 A 364 ILE ALA GLU PRO LEU LYS LYS VAL ILE PRO VAL LYS LEU SEQRES 7 A 364 VAL ILE PRO GLY LEU LEU PHE ILE ASP THR PRO GLY HIS SEQRES 8 A 364 GLU LEU PHE SER ASN LEU ARG ARG ARG GLY GLY SER VAL SEQRES 9 A 364 ALA ASP PHE ALA ILE LEU VAL VAL ASP ILE MET GLU GLY SEQRES 10 A 364 PHE LYS PRO GLN THR TYR GLU ALA LEU GLU LEU LEU LYS SEQRES 11 A 364 GLU ARG ARG VAL PRO PHE LEU ILE ALA ALA ASN LYS ILE SEQRES 12 A 364 ASP ARG ILE PRO GLY TRP LYS PRO ASN PRO ASP ALA PRO SEQRES 13 A 364 PHE ILE GLU THR ILE ARG ARG GLN ASP PRO LYS VAL ARG SEQRES 14 A 364 GLU ILE LEU GLU GLN ARG VAL TYR GLU ILE VAL GLY LYS SEQRES 15 A 364 MET TYR GLU ALA GLY LEU PRO ALA GLU LEU PHE THR ARG SEQRES 16 A 364 ILE LYS ASP PHE ARG ARG LYS ILE ALA ILE VAL PRO VAL SEQRES 17 A 364 SER ALA ARG THR GLY GLU GLY ILE PRO GLU LEU LEU ALA SEQRES 18 A 364 VAL LEU ALA GLY LEU THR GLN THR TYR LEU LYS GLU ARG SEQRES 19 A 364 LEU ARG TYR ALA GLU GLY PRO ALA LYS GLY VAL VAL LEU SEQRES 20 A 364 GLU VAL LYS GLU MET GLN GLY PHE GLY THR VAL VAL ASP SEQRES 21 A 364 ALA VAL ILE TYR ASP GLY VAL LEU LYS LYS GLU ASP ILE SEQRES 22 A 364 ILE VAL VAL GLY GLY ARG GLU GLY PRO ILE VAL THR ARG SEQRES 23 A 364 VAL ARG ALA LEU LEU MET PRO ALA PRO LEU GLN ASP ILE SEQRES 24 A 364 ARG SER ARG GLU ALA ARG PHE VAL GLN VAL ASP ARG VAL SEQRES 25 A 364 TYR ALA ALA ALA GLY VAL ARG ILE ALA ALA PRO GLY LEU SEQRES 26 A 364 ASP ASP VAL ILE ALA GLY SER PRO ILE TYR ALA ALA GLU SEQRES 27 A 364 SER GLU GLU GLU ALA ARG LYS LEU MET GLU ALA VAL GLN SEQRES 28 A 364 ARG GLU ILE GLU GLU LEU ARG HIS HIS HIS HIS HIS HIS SEQRES 1 B 21 LYS LYS LYS LYS LYS LYS GLU GLU GLU VAL ASP LEU SER SEQRES 2 B 21 GLY LEU SER GLY MET PHE GLY PHE HET GDP A 500 28 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE FORMUL 3 GDP C10 H15 N5 O11 P2 FORMUL 4 HOH *151(H2 O) HELIX 1 AA1 GLY A 28 ALA A 43 1 16 HELIX 2 AA2 ALA A 60 ALA A 67 1 8 HELIX 3 AA3 GLU A 68 LYS A 71 5 4 HELIX 4 AA4 GLY A 90 ASN A 96 1 7 HELIX 5 AA5 LYS A 119 ARG A 133 1 15 HELIX 6 AA6 LYS A 142 ILE A 146 5 5 HELIX 7 AA7 PRO A 156 ARG A 163 1 8 HELIX 8 AA8 ASP A 165 ALA A 186 1 22 HELIX 9 AA9 THR A 194 ILE A 196 5 3 HELIX 10 AB1 GLY A 215 LEU A 231 1 17 HELIX 11 AB2 LEU A 231 ARG A 236 1 6 HELIX 12 AB3 SER A 339 ARG A 358 1 20 HELIX 13 AB4 GLY B 104 PHE B 109 5 6 SHEET 1 AA1 8 THR A 50 HIS A 52 0 SHEET 2 AA1 8 ALA A 55 PRO A 59 -1 O ILE A 57 N THR A 50 SHEET 3 AA1 8 GLY A 82 ILE A 86 -1 O LEU A 83 N VAL A 58 SHEET 4 AA1 8 ILE A 18 GLY A 23 1 N VAL A 19 O LEU A 84 SHEET 5 AA1 8 PHE A 107 ASP A 113 1 O VAL A 111 N LEU A 22 SHEET 6 AA1 8 PHE A 136 ASN A 141 1 O LEU A 137 N LEU A 110 SHEET 7 AA1 8 ILE A 203 PRO A 207 1 O VAL A 206 N ILE A 138 SHEET 8 AA1 8 ALA A 190 LEU A 192 1 N GLU A 191 O ILE A 203 SHEET 1 AA2 8 GLY A 281 ARG A 286 0 SHEET 2 AA2 8 ILE A 273 GLY A 278 -1 N VAL A 276 O ILE A 283 SHEET 3 AA2 8 PRO A 333 ALA A 337 -1 O ALA A 337 N ILE A 273 SHEET 4 AA2 8 LYS A 243 MET A 252 -1 N GLY A 244 O ILE A 334 SHEET 5 AA2 8 GLY A 256 ASP A 265 -1 O ASP A 260 N LEU A 247 SHEET 6 AA2 8 ALA A 316 ALA A 321 -1 O ILE A 320 N VAL A 259 SHEET 7 AA2 8 ALA A 289 MET A 292 -1 N LEU A 291 O ARG A 319 SHEET 8 AA2 8 VAL A 307 VAL A 309 -1 O VAL A 307 N MET A 292 SHEET 1 AA3 2 VAL A 267 LYS A 269 0 SHEET 2 AA3 2 ARG A 311 TYR A 313 -1 O VAL A 312 N LEU A 268 CISPEP 1 ALA A 314 ALA A 315 0 -1.17 SITE 1 AC1 21 HIS A 24 ASP A 26 HIS A 27 GLY A 28 SITE 2 AC1 21 LYS A 29 THR A 30 THR A 31 ASN A 141 SITE 3 AC1 21 LYS A 142 ASP A 144 ARG A 145 GLU A 159 SITE 4 AC1 21 ARG A 163 SER A 209 ALA A 210 ARG A 211 SITE 5 AC1 21 HOH A 656 HOH A 661 HOH A 691 HOH A 696 SITE 6 AC1 21 PHE B 111 CRYST1 54.720 79.016 101.510 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 0.018275 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012656 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009851 0.00000