PDB Short entry for 5DL5 HEADER MEMBRANE PROTEIN 04-SEP-15 5DL5 TITLE CRYSTAL STRUCTURE OF ACINETOBACTER BAUMANNII OCCAB1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MEMBRANE PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ACINETOBACTER BAUMANNII AB307-0294; SOURCE 3 ORGANISM_TAXID: 557600; SOURCE 4 GENE: VM83_01045; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS OUTER MEMBRANE PROTEIN, BETA-BARREL, ANTIBIOTIC UPTAKE, MEMBRANE KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.ZAHN,A.BASLE,B.VAN DEN BERG REVDAT 3 10-JAN-24 5DL5 1 REMARK REVDAT 2 10-FEB-16 5DL5 1 JRNL REVDAT 1 03-FEB-16 5DL5 0 JRNL AUTH M.ZAHN,S.P.BHAMIDIMARRI,A.BASLE,M.WINTERHALTER, JRNL AUTH 2 B.VAN DEN BERG JRNL TITL STRUCTURAL INSIGHTS INTO OUTER MEMBRANE PERMEABILITY OF JRNL TITL 2 ACINETOBACTER BAUMANNII. JRNL REF STRUCTURE V. 24 221 2016 JRNL REFN ISSN 0969-2126 JRNL PMID 26805524 JRNL DOI 10.1016/J.STR.2015.12.009 REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0131 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 116.11 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 33329 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) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1705 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) : 2.05 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.10 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2375 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.79 REMARK 3 BIN R VALUE (WORKING SET) : 0.2370 REMARK 3 BIN FREE R VALUE SET COUNT : 108 REMARK 3 BIN FREE R VALUE : 0.2480 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3232 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 42 REMARK 3 SOLVENT ATOMS : 76 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.53 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : -0.01000 REMARK 3 B33 (A**2) : 0.03000 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): 0.163 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.146 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.100 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.630 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.940 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3345 ; 0.025 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3034 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4520 ; 2.267 ; 1.930 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6958 ; 1.109 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 415 ; 7.262 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 169 ;39.619 ;24.675 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 510 ;14.241 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;14.043 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 469 ; 0.151 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3923 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 836 ; 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): 1663 ; 1.985 ; 2.633 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1662 ; 1.982 ; 2.632 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2077 ; 2.668 ; 3.935 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2078 ; 2.668 ; 3.936 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1682 ; 3.336 ; 3.096 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1679 ; 3.291 ; 3.091 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2438 ; 4.894 ; 4.463 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3606 ; 6.533 ;22.231 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3607 ; 6.533 ;22.237 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 : 3 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 0 A 179 REMARK 3 ORIGIN FOR THE GROUP (A): -17.0763 -54.7884 2.6498 REMARK 3 T TENSOR REMARK 3 T11: 0.0137 T22: 0.0831 REMARK 3 T33: 0.0709 T12: -0.0155 REMARK 3 T13: 0.0082 T23: -0.0457 REMARK 3 L TENSOR REMARK 3 L11: 1.1352 L22: 2.6154 REMARK 3 L33: 0.6100 L12: -0.1910 REMARK 3 L13: 0.0720 L23: -0.8902 REMARK 3 S TENSOR REMARK 3 S11: -0.0107 S12: -0.0116 S13: 0.0356 REMARK 3 S21: 0.0578 S22: 0.0058 S23: 0.1083 REMARK 3 S31: -0.0585 S32: -0.0608 S33: 0.0049 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 180 A 222 REMARK 3 ORIGIN FOR THE GROUP (A): 4.0586 -55.9012 11.3280 REMARK 3 T TENSOR REMARK 3 T11: 0.0697 T22: 0.1129 REMARK 3 T33: 0.1073 T12: -0.0246 REMARK 3 T13: 0.0207 T23: -0.0166 REMARK 3 L TENSOR REMARK 3 L11: 3.2220 L22: 2.6976 REMARK 3 L33: 4.3456 L12: 1.4605 REMARK 3 L13: 2.3727 L23: 0.4630 REMARK 3 S TENSOR REMARK 3 S11: -0.0051 S12: -0.4048 S13: 0.0350 REMARK 3 S21: 0.2840 S22: -0.1558 S23: -0.0540 REMARK 3 S31: -0.2706 S32: -0.0884 S33: 0.1609 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 223 A 415 REMARK 3 ORIGIN FOR THE GROUP (A): -0.0644 -43.8566 -1.7062 REMARK 3 T TENSOR REMARK 3 T11: 0.0421 T22: 0.0803 REMARK 3 T33: 0.0684 T12: -0.0252 REMARK 3 T13: -0.0111 T23: -0.0126 REMARK 3 L TENSOR REMARK 3 L11: 2.3812 L22: 1.7141 REMARK 3 L33: 1.0952 L12: 0.0763 REMARK 3 L13: -0.2902 L23: -0.0724 REMARK 3 S TENSOR REMARK 3 S11: -0.0935 S12: 0.0256 S13: 0.1684 REMARK 3 S21: -0.0338 S22: 0.0525 S23: -0.0753 REMARK 3 S31: -0.1232 S32: -0.1133 S33: 0.0410 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 5DL5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-SEP-15. REMARK 100 THE DEPOSITION ID IS D_1000213352. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-DEC-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35036 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 116.110 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.30 REMARK 200 R MERGE FOR SHELL (I) : 0.68300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100 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: 3SYS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 32% PEG 400, 0.2 M AMMONIUM PHOSPHATE, REMARK 280 0.1 M AMMONIUM SULPHATE, 0.1 M SODIUM CITRATE PH 4.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 6 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z REMARK 290 6555 X-Y,X,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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 KCAL/MOL 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 ALA A -14 REMARK 465 ASN A -13 REMARK 465 VAL A -12 REMARK 465 ARG A -11 REMARK 465 LEU A -10 REMARK 465 GLN A -9 REMARK 465 HIS A -8 REMARK 465 HIS A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 LEU A -1 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 SER A 191 CB SER A 191 OG -0.080 REMARK 500 TYR A 238 CG TYR A 238 CD2 0.096 REMARK 500 TYR A 302 CB TYR A 302 CG 0.091 REMARK 500 SER A 390 CB SER A 390 OG -0.091 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 64 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP A 116 CB - CG - OD1 ANGL. DEV. = 6.6 DEGREES REMARK 500 ASP A 166 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP A 186 CB - CG - OD1 ANGL. DEV. = -7.0 DEGREES REMARK 500 ARG A 203 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG A 203 NE - CZ - NH2 ANGL. DEV. = -4.4 DEGREES REMARK 500 HIS A 274 N - CA - CB ANGL. DEV. = -13.4 DEGREES REMARK 500 ARG A 381 NE - CZ - NH1 ANGL. DEV. = 3.1 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 SER A 104 -117.29 55.59 REMARK 500 LEU A 120 79.55 -156.23 REMARK 500 ARG A 126 -138.35 -122.24 REMARK 500 ASP A 173 -73.97 -84.37 REMARK 500 ASN A 185 -168.82 -161.02 REMARK 500 ALA A 200 -64.96 -128.94 REMARK 500 ASN A 294 48.93 -144.83 REMARK 500 TYR A 307 -109.42 -136.96 REMARK 500 LEU A 333 104.70 -168.35 REMARK 500 ASP A 377 -2.76 72.33 REMARK 500 GLN A 394 -92.71 -109.50 REMARK 500 TYR A 397 -94.12 -147.50 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 PRO A 273 HIS A 274 -147.14 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 C8E A 501 REMARK 610 C8E A 502 REMARK 610 C8E A 503 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue C8E A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue C8E A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue C8E A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 504 DBREF1 5DL5 A 1 415 UNP A0A0F5EN03_ACIBA DBREF2 5DL5 A A0A0F5EN03 37 451 SEQADV 5DL5 ALA A -14 UNP A0A0F5EN0 EXPRESSION TAG SEQADV 5DL5 ASN A -13 UNP A0A0F5EN0 EXPRESSION TAG SEQADV 5DL5 VAL A -12 UNP A0A0F5EN0 EXPRESSION TAG SEQADV 5DL5 ARG A -11 UNP A0A0F5EN0 EXPRESSION TAG SEQADV 5DL5 LEU A -10 UNP A0A0F5EN0 EXPRESSION TAG SEQADV 5DL5 GLN A -9 UNP A0A0F5EN0 EXPRESSION TAG SEQADV 5DL5 HIS A -8 UNP A0A0F5EN0 EXPRESSION TAG SEQADV 5DL5 HIS A -7 UNP A0A0F5EN0 EXPRESSION TAG SEQADV 5DL5 HIS A -6 UNP A0A0F5EN0 EXPRESSION TAG SEQADV 5DL5 HIS A -5 UNP A0A0F5EN0 EXPRESSION TAG SEQADV 5DL5 HIS A -4 UNP A0A0F5EN0 EXPRESSION TAG SEQADV 5DL5 HIS A -3 UNP A0A0F5EN0 EXPRESSION TAG SEQADV 5DL5 HIS A -2 UNP A0A0F5EN0 EXPRESSION TAG SEQADV 5DL5 LEU A -1 UNP A0A0F5EN0 EXPRESSION TAG SEQADV 5DL5 GLU A 0 UNP A0A0F5EN0 EXPRESSION TAG SEQRES 1 A 430 ALA ASN VAL ARG LEU GLN HIS HIS HIS HIS HIS HIS HIS SEQRES 2 A 430 LEU GLU SER GLU GLN SER GLU ALA LYS GLY PHE VAL GLU SEQRES 3 A 430 ASP ALA ASN GLY SER ILE LEU PHE ARG THR GLY TYR LEU SEQRES 4 A 430 THR ARG ASP LYS LYS GLN GLY ALA LYS ASP THR SER SER SEQRES 5 A 430 VAL ALA GLN SER ALA ILE VAL SER ILE GLU SER GLY PHE SEQRES 6 A 430 THR PRO GLY ILE VAL GLY PHE GLY VAL GLY VAL VAL GLY SEQRES 7 A 430 ASP GLY SER PHE LYS ILE GLY GLU ASN LYS ASN ALA GLY SEQRES 8 A 430 ASN GLN MET ILE PRO LYS HIS ASN ASP GLY SER ALA TYR SEQRES 9 A 430 ASP HIS TRP ALA ARG GLY GLY GLY SER VAL LYS ALA ARG SEQRES 10 A 430 PHE SER ASN THR THR VAL ARG TYR GLY THR GLN VAL LEU SEQRES 11 A 430 ASP LEU PRO VAL LEU ALA SER ASN THR GLY ARG MET VAL SEQRES 12 A 430 PRO GLU TYR PHE THR GLY THR LEU LEU THR SER HIS GLU SEQRES 13 A 430 ILE LYS ASN LEU GLU VAL VAL ALA GLY LYS PHE THR LYS SEQRES 14 A 430 ASP GLN MET SER ASP GLN ILE ASN THR ASP ALA ASP ALA SEQRES 15 A 430 SER GLY ARG GLY LEU ASP ARG ALA ILE VAL TRP GLY ALA SEQRES 16 A 430 LYS TYR LYS PHE ASN ASP ASN LEU ASN ALA SER TYR TYR SEQRES 17 A 430 GLY LEU ASP SER LYS ASN ALA LEU GLU ARG HIS TYR ALA SEQRES 18 A 430 ASN VAL ASN PHE LYS GLN PRO LEU ALA ASN ASP SER SER SEQRES 19 A 430 LEU THR TYR ASP PHE SER GLY TYR HIS THR LYS PHE ASP SEQRES 20 A 430 ALA ASN ALA HIS THR TYR SER ALA THR GLY THR VAL ALA SEQRES 21 A 430 PRO ASN TYR ALA ALA ASP GLY ILE ALA GLY GLU GLU LYS SEQRES 22 A 430 THR ASN ASN ILE TRP ALA ILE SER GLY THR TYR ALA THR SEQRES 23 A 430 GLY PRO HIS SER VAL MET LEU ALA TYR GLN GLN ASN THR SEQRES 24 A 430 GLY ASN VAL GLY TYR ASP TYR GLY GLN ASN ALA ASP GLY SEQRES 25 A 430 PHE GLN SER ILE TYR LEU PRO ASN SER TYR MET SER ASP SEQRES 26 A 430 PHE ILE GLY ASN HIS GLU LYS SER ALA GLN ILE GLN TYR SEQRES 27 A 430 ASN VAL ASP PHE GLY LYS LEU GLY VAL LEU PRO GLY LEU SEQRES 28 A 430 ASN TRP THR THR ALA PHE VAL TYR GLY TRP ASP ILE LYS SEQRES 29 A 430 VAL ARG ASN VAL THR ASP ASP ALA GLN GLU ARG GLU PHE SEQRES 30 A 430 PHE ASN GLN VAL LYS TYR THR VAL GLN SER GLY PHE ALA SEQRES 31 A 430 LYS ASP ALA SER LEU ARG ILE ARG ASN SER TYR TYR ARG SEQRES 32 A 430 ALA SER ASP ALA TYR GLN GLY ALA TYR ILE GLY ASP THR SEQRES 33 A 430 ASN GLU TRP ARG ILE PHE LEU ASP ILE PRO VAL LYS LEU SEQRES 34 A 430 PHE HET C8E A 501 16 HET C8E A 502 14 HET C8E A 503 7 HET PO4 A 504 5 HETNAM C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE HETNAM PO4 PHOSPHATE ION FORMUL 2 C8E 3(C16 H34 O5) FORMUL 5 PO4 O4 P 3- FORMUL 6 HOH *76(H2 O) HELIX 1 AA1 ASN A 247 GLY A 252 1 6 SHEET 1 AA119 ASN A 14 LYS A 28 0 SHEET 2 AA119 THR A 35 GLU A 47 -1 O GLU A 47 N ASN A 14 SHEET 3 AA119 VAL A 55 LYS A 68 -1 O GLY A 63 N VAL A 44 SHEET 4 AA119 HIS A 91 PHE A 103 -1 O ARG A 102 N GLY A 56 SHEET 5 AA119 THR A 106 GLN A 113 -1 O THR A 112 N GLY A 97 SHEET 6 AA119 TYR A 131 ILE A 142 -1 O PHE A 132 N GLN A 113 SHEET 7 AA119 LEU A 145 GLN A 156 -1 O ALA A 149 N LEU A 137 SHEET 8 AA119 ALA A 175 ASN A 185 -1 O ALA A 175 N PHE A 152 SHEET 9 AA119 LEU A 188 SER A 197 -1 O GLY A 194 N TRP A 178 SHEET 10 AA119 LEU A 201 LEU A 214 -1 O LEU A 201 N SER A 197 SHEET 11 AA119 SER A 218 PHE A 231 -1 O LEU A 220 N GLN A 212 SHEET 12 AA119 LYS A 258 THR A 271 -1 O LYS A 258 N PHE A 231 SHEET 13 AA119 HIS A 274 GLY A 285 -1 O THR A 284 N ASN A 261 SHEET 14 AA119 LYS A 317 ASP A 326 -1 O ASN A 324 N SER A 275 SHEET 15 AA119 LEU A 336 VAL A 350 -1 O THR A 340 N TYR A 323 SHEET 16 AA119 THR A 354 THR A 369 -1 O GLU A 359 N GLY A 345 SHEET 17 AA119 SER A 379 ALA A 389 -1 O ASN A 384 N ASN A 364 SHEET 18 AA119 THR A 401 PHE A 415 -1 O THR A 401 N TYR A 387 SHEET 19 AA119 ASN A 14 LYS A 28 -1 N THR A 21 O LEU A 408 SHEET 1 AA2 2 ASP A 116 LEU A 117 0 SHEET 2 AA2 2 LEU A 120 ALA A 121 -1 O LEU A 120 N LEU A 117 SITE 1 AC1 11 ARG A 26 GLY A 76 ASN A 77 GLN A 78 SITE 2 AC1 11 LYS A 82 ARG A 126 TYR A 307 MET A 308 SITE 3 AC1 11 ARG A 405 HOH A 608 HOH A 653 SITE 1 AC2 7 GLN A 40 GLY A 65 PHE A 67 HIS A 91 SITE 2 AC2 7 TRP A 92 ALA A 93 C8E A 503 SITE 1 AC3 4 PHE A 67 TYR A 280 GLN A 282 C8E A 502 SITE 1 AC4 4 HIS A 83 TYR A 89 ASP A 90 HIS A 91 CRYST1 134.073 134.073 54.410 90.00 90.00 120.00 P 6 6 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 0.007459 0.004306 0.000000 0.00000 SCALE2 0.000000 0.008612 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018379 0.00000