HEADER UNKNOWN FUNCTION 23-MAR-16 5IXG TITLE CRYSTAL STRUCTURE OF BURKHOLDERIA CENOCEPACIA BCNB COMPND MOL_ID: 1; COMPND 2 MOLECULE: YCEI; COMPND 3 CHAIN: B, C, A, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BURKHOLDERIA CENOCEPACIA PC184; SOURCE 3 ORGANISM_TAXID: 350702; SOURCE 4 GENE: BCPG_01022; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS BETA BARREL LIPOCALIN, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR S.A.LOUTET,M.E.P.MURPHY REVDAT 4 27-SEP-23 5IXG 1 REMARK REVDAT 3 08-JAN-20 5IXG 1 REMARK REVDAT 2 29-MAR-17 5IXG 1 JRNL REMARK REVDAT 1 22-MAR-17 5IXG 0 JRNL AUTH O.M.EL-HALFAWY,J.KLETT,R.J.INGRAM,S.A.LOUTET,M.E.MURPHY, JRNL AUTH 2 S.MARTIN-SANTAMARIA,M.A.VALVANO JRNL TITL ANTIBIOTIC CAPTURE BY BACTERIAL LIPOCALINS UNCOVERS AN JRNL TITL 2 EXTRACELLULAR MECHANISM OF INTRINSIC ANTIBIOTIC RESISTANCE. JRNL REF MBIO V. 8 2017 JRNL REFN ESSN 2150-7511 JRNL PMID 28292982 JRNL DOI 10.1128/MBIO.00225-17 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.33 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 77882 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) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4090 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4728 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 80.39 REMARK 3 BIN R VALUE (WORKING SET) : 0.1870 REMARK 3 BIN FREE R VALUE SET COUNT : 252 REMARK 3 BIN FREE R VALUE : 0.2440 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5218 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 203 REMARK 3 SOLVENT ATOMS : 482 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.25 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.19000 REMARK 3 B22 (A**2) : 0.65000 REMARK 3 B33 (A**2) : 0.52000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.07000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.087 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.088 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.053 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.263 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.952 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5623 ; 0.024 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 5376 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7594 ; 2.391 ; 1.984 REMARK 3 BOND ANGLES OTHERS (DEGREES): 12429 ; 0.950 ; 3.002 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 689 ; 6.471 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 228 ;31.021 ;24.254 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 923 ;14.027 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;14.176 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 805 ; 0.143 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6284 ; 0.012 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1263 ; 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): 2735 ; 1.860 ; 1.354 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2734 ; 1.860 ; 1.353 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3425 ; 2.812 ; 2.025 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3426 ; 2.812 ; 2.026 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2888 ; 3.465 ; 1.906 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2889 ; 3.465 ; 1.907 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4164 ; 5.227 ; 2.678 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 6346 ; 7.044 ;13.034 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 6319 ; 7.032 ;12.980 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 : 4 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 : B 6 B 174 REMARK 3 ORIGIN FOR THE GROUP (A): 47.7779 27.8148 3.7445 REMARK 3 T TENSOR REMARK 3 T11: 0.0394 T22: 0.0261 REMARK 3 T33: 0.0401 T12: 0.0042 REMARK 3 T13: -0.0030 T23: 0.0051 REMARK 3 L TENSOR REMARK 3 L11: 0.3555 L22: 0.0361 REMARK 3 L33: 0.2235 L12: 0.0976 REMARK 3 L13: 0.0163 L23: -0.0338 REMARK 3 S TENSOR REMARK 3 S11: -0.0508 S12: 0.0214 S13: -0.0162 REMARK 3 S21: -0.0059 S22: 0.0128 S23: -0.0072 REMARK 3 S31: -0.0140 S32: 0.0061 S33: 0.0380 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 : C 6 C 174 REMARK 3 ORIGIN FOR THE GROUP (A): 50.3277 36.0173 32.6319 REMARK 3 T TENSOR REMARK 3 T11: 0.0418 T22: 0.0417 REMARK 3 T33: 0.0565 T12: -0.0050 REMARK 3 T13: -0.0066 T23: 0.0269 REMARK 3 L TENSOR REMARK 3 L11: 0.2715 L22: 0.0274 REMARK 3 L33: 0.6051 L12: -0.0343 REMARK 3 L13: -0.1271 L23: -0.0694 REMARK 3 S TENSOR REMARK 3 S11: 0.0222 S12: 0.0121 S13: 0.0756 REMARK 3 S21: -0.0277 S22: 0.0213 S23: 0.0102 REMARK 3 S31: 0.1278 S32: -0.0412 S33: -0.0435 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 7 A 174 REMARK 3 ORIGIN FOR THE GROUP (A): 71.9825 27.2102 4.1988 REMARK 3 T TENSOR REMARK 3 T11: 0.0392 T22: 0.0353 REMARK 3 T33: 0.0300 T12: 0.0009 REMARK 3 T13: -0.0042 T23: 0.0169 REMARK 3 L TENSOR REMARK 3 L11: 0.5982 L22: 0.1224 REMARK 3 L33: 0.0686 L12: -0.0549 REMARK 3 L13: -0.0174 L23: 0.0901 REMARK 3 S TENSOR REMARK 3 S11: -0.0435 S12: 0.0328 S13: -0.0145 REMARK 3 S21: 0.0297 S22: 0.0133 S23: 0.0331 REMARK 3 S31: 0.0145 S32: 0.0110 S33: 0.0303 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 6 D 174 REMARK 3 ORIGIN FOR THE GROUP (A): 68.9472 48.6194 24.7134 REMARK 3 T TENSOR REMARK 3 T11: 0.0629 T22: 0.0541 REMARK 3 T33: 0.0385 T12: -0.0084 REMARK 3 T13: 0.0264 T23: 0.0082 REMARK 3 L TENSOR REMARK 3 L11: 0.5135 L22: 0.4805 REMARK 3 L33: 0.5496 L12: 0.2542 REMARK 3 L13: -0.4925 L23: -0.4072 REMARK 3 S TENSOR REMARK 3 S11: 0.0811 S12: -0.1128 S13: 0.0793 REMARK 3 S21: -0.0892 S22: -0.0224 S23: 0.0370 REMARK 3 S31: -0.0071 S32: 0.1044 S33: -0.0587 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 5IXG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1000219573. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-JUN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97949 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.1.26 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 82019 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 37.330 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.29800 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: PHASER 2.5.5 REMARK 200 STARTING MODEL: 1WUB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HEPES, PEG 6000, PH 6.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 50.58500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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: 6760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 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: 6620 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 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 SER A 6 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 O1 OTP B 201 O HOH B 301 1.92 REMARK 500 OD1 ASP C 96 O HOH C 301 2.05 REMARK 500 O HOH D 352 O HOH D 382 2.15 REMARK 500 O HOH B 348 O HOH B 360 2.19 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 TYR C 89 CE1 TYR C 89 CZ -0.106 REMARK 500 ASP A 139 CB ASP A 139 CG 0.127 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 LYS B 94 CD - CE - NZ ANGL. DEV. = -14.8 DEGREES REMARK 500 ASP B 96 CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 ARG B 146 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG B 146 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 CYS C 125 CA - CB - SG ANGL. DEV. = 6.9 DEGREES REMARK 500 ASP C 147 CB - CG - OD1 ANGL. DEV. = 7.1 DEGREES REMARK 500 ARG A 32 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 ASP A 70 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 ASP D 36 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 ASP D 147 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES REMARK 500 ASP D 147 CB - CG - OD2 ANGL. DEV. = -6.0 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 B 78 -103.71 -136.27 REMARK 500 LYS B 132 -39.31 75.42 REMARK 500 LEU B 151 75.74 -102.48 REMARK 500 ASP C 45 78.42 -119.55 REMARK 500 ALA C 47 -50.66 -140.88 REMARK 500 PHE C 78 -99.37 -125.45 REMARK 500 ASP C 80 70.97 49.64 REMARK 500 LEU C 151 71.91 -114.04 REMARK 500 PHE A 78 -108.68 -144.27 REMARK 500 ASP A 96 73.49 -113.10 REMARK 500 LEU A 151 77.65 -107.73 REMARK 500 PHE D 78 -99.29 -142.43 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 ASP D 98 LYS D 99 -148.82 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 448 DISTANCE = 5.95 ANGSTROMS REMARK 525 HOH A 442 DISTANCE = 6.12 ANGSTROMS REMARK 525 HOH D 396 DISTANCE = 5.84 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue OTP B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue OTP C 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue OTP A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue OTP D 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5IXH RELATED DB: PDB DBREF 5IXG A 6 174 UNP A2VST2 A2VST2_9BURK 24 192 DBREF 5IXG B 6 174 UNP A2VST2 A2VST2_9BURK 24 192 DBREF 5IXG C 6 174 UNP A2VST2 A2VST2_9BURK 24 192 DBREF 5IXG D 6 174 UNP A2VST2 A2VST2_9BURK 24 192 SEQRES 1 B 169 SER ALA THR TYR GLN PHE ASP PRO SER HIS THR TYR PRO SEQRES 2 B 169 SER PHE GLU ALA ASP HIS PHE GLY GLY LEU SER VAL TRP SEQRES 3 B 169 ARG GLY LYS PHE ASP LYS SER SER GLY THR VAL THR LEU SEQRES 4 B 169 ASP ARG ALA ALA LYS THR GLY THR VAL ASP VAL THR THR SEQRES 5 B 169 ASP ILE ALA SER ILE HIS THR GLY SER ALA LYS LEU ASP SEQRES 6 B 169 GLU HIS LEU GLN THR ALA GLU PHE PHE ASP ALA ALA LYS SEQRES 7 B 169 PHE PRO GLN ALA ASN TYR LYS GLY THR ILE LYS PHE ASP SEQRES 8 B 169 GLY ASP LYS PRO VAL SER VAL VAL GLY ASN LEU THR LEU SEQRES 9 B 169 HIS GLY VAL THR LYS PRO LEU THR LEU LYS ILE ASP SER SEQRES 10 B 169 PHE LYS CYS MET PRO HIS PRO MET LEU LYS ARG GLU VAL SEQRES 11 B 169 CYS GLY VAL ASP ALA VAL GLY GLU PHE SER ARG ASP ASP SEQRES 12 B 169 PHE GLY LEU ASP TYR GLY LYS GLN TYR GLY PHE LYS MET SEQRES 13 B 169 LYS THR LYS LEU LEU ILE THR ALA GLU ALA VAL LYS GLN SEQRES 1 C 169 SER ALA THR TYR GLN PHE ASP PRO SER HIS THR TYR PRO SEQRES 2 C 169 SER PHE GLU ALA ASP HIS PHE GLY GLY LEU SER VAL TRP SEQRES 3 C 169 ARG GLY LYS PHE ASP LYS SER SER GLY THR VAL THR LEU SEQRES 4 C 169 ASP ARG ALA ALA LYS THR GLY THR VAL ASP VAL THR THR SEQRES 5 C 169 ASP ILE ALA SER ILE HIS THR GLY SER ALA LYS LEU ASP SEQRES 6 C 169 GLU HIS LEU GLN THR ALA GLU PHE PHE ASP ALA ALA LYS SEQRES 7 C 169 PHE PRO GLN ALA ASN TYR LYS GLY THR ILE LYS PHE ASP SEQRES 8 C 169 GLY ASP LYS PRO VAL SER VAL VAL GLY ASN LEU THR LEU SEQRES 9 C 169 HIS GLY VAL THR LYS PRO LEU THR LEU LYS ILE ASP SER SEQRES 10 C 169 PHE LYS CYS MET PRO HIS PRO MET LEU LYS ARG GLU VAL SEQRES 11 C 169 CYS GLY VAL ASP ALA VAL GLY GLU PHE SER ARG ASP ASP SEQRES 12 C 169 PHE GLY LEU ASP TYR GLY LYS GLN TYR GLY PHE LYS MET SEQRES 13 C 169 LYS THR LYS LEU LEU ILE THR ALA GLU ALA VAL LYS GLN SEQRES 1 A 169 SER ALA THR TYR GLN PHE ASP PRO SER HIS THR TYR PRO SEQRES 2 A 169 SER PHE GLU ALA ASP HIS PHE GLY GLY LEU SER VAL TRP SEQRES 3 A 169 ARG GLY LYS PHE ASP LYS SER SER GLY THR VAL THR LEU SEQRES 4 A 169 ASP ARG ALA ALA LYS THR GLY THR VAL ASP VAL THR THR SEQRES 5 A 169 ASP ILE ALA SER ILE HIS THR GLY SER ALA LYS LEU ASP SEQRES 6 A 169 GLU HIS LEU GLN THR ALA GLU PHE PHE ASP ALA ALA LYS SEQRES 7 A 169 PHE PRO GLN ALA ASN TYR LYS GLY THR ILE LYS PHE ASP SEQRES 8 A 169 GLY ASP LYS PRO VAL SER VAL VAL GLY ASN LEU THR LEU SEQRES 9 A 169 HIS GLY VAL THR LYS PRO LEU THR LEU LYS ILE ASP SER SEQRES 10 A 169 PHE LYS CYS MET PRO HIS PRO MET LEU LYS ARG GLU VAL SEQRES 11 A 169 CYS GLY VAL ASP ALA VAL GLY GLU PHE SER ARG ASP ASP SEQRES 12 A 169 PHE GLY LEU ASP TYR GLY LYS GLN TYR GLY PHE LYS MET SEQRES 13 A 169 LYS THR LYS LEU LEU ILE THR ALA GLU ALA VAL LYS GLN SEQRES 1 D 169 SER ALA THR TYR GLN PHE ASP PRO SER HIS THR TYR PRO SEQRES 2 D 169 SER PHE GLU ALA ASP HIS PHE GLY GLY LEU SER VAL TRP SEQRES 3 D 169 ARG GLY LYS PHE ASP LYS SER SER GLY THR VAL THR LEU SEQRES 4 D 169 ASP ARG ALA ALA LYS THR GLY THR VAL ASP VAL THR THR SEQRES 5 D 169 ASP ILE ALA SER ILE HIS THR GLY SER ALA LYS LEU ASP SEQRES 6 D 169 GLU HIS LEU GLN THR ALA GLU PHE PHE ASP ALA ALA LYS SEQRES 7 D 169 PHE PRO GLN ALA ASN TYR LYS GLY THR ILE LYS PHE ASP SEQRES 8 D 169 GLY ASP LYS PRO VAL SER VAL VAL GLY ASN LEU THR LEU SEQRES 9 D 169 HIS GLY VAL THR LYS PRO LEU THR LEU LYS ILE ASP SER SEQRES 10 D 169 PHE LYS CYS MET PRO HIS PRO MET LEU LYS ARG GLU VAL SEQRES 11 D 169 CYS GLY VAL ASP ALA VAL GLY GLU PHE SER ARG ASP ASP SEQRES 12 D 169 PHE GLY LEU ASP TYR GLY LYS GLN TYR GLY PHE LYS MET SEQRES 13 D 169 LYS THR LYS LEU LEU ILE THR ALA GLU ALA VAL LYS GLN HET OTP B 201 49 HET PEG B 202 7 HET OTP C 201 49 HET OTP A 201 49 HET OTP D 201 49 HETNAM OTP (2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31- HETNAM 2 OTP OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL HETNAM 3 OTP TRIHYDROGEN DIPHOSPHATE HETNAM PEG DI(HYDROXYETHYL)ETHER HETSYN OTP OCTAPRENYL PYROPHOSPHATE FORMUL 5 OTP 4(C40 H68 O7 P2) FORMUL 6 PEG C4 H10 O3 FORMUL 10 HOH *482(H2 O) HELIX 1 AA1 PRO B 13 THR B 16 5 4 HELIX 2 AA2 SER B 66 GLN B 74 1 9 HELIX 3 AA3 ASP B 147 GLY B 150 5 4 HELIX 4 AA4 GLY B 154 GLY B 158 5 5 HELIX 5 AA5 PRO C 13 THR C 16 5 4 HELIX 6 AA6 SER C 66 THR C 75 1 10 HELIX 7 AA7 ASP C 147 GLY C 150 5 4 HELIX 8 AA8 GLY C 154 GLY C 158 5 5 HELIX 9 AA9 PRO A 13 THR A 16 5 4 HELIX 10 AB1 SER A 66 THR A 75 1 10 HELIX 11 AB2 ASP A 147 GLY A 150 5 4 HELIX 12 AB3 GLY A 154 GLY A 158 5 5 HELIX 13 AB4 PRO D 13 THR D 16 5 4 HELIX 14 AB5 SER D 66 LEU D 73 1 8 HELIX 15 AB6 ASP D 147 GLY D 150 5 4 HELIX 16 AB7 GLY D 154 GLY D 158 5 5 SHEET 1 AA112 ILE B 62 HIS B 63 0 SHEET 2 AA112 SER B 29 PHE B 35 -1 N LYS B 34 O HIS B 63 SHEET 3 AA112 TYR B 17 HIS B 24 -1 N PHE B 20 O GLY B 33 SHEET 4 AA112 LYS B 162 LYS B 173 -1 O LEU B 166 N SER B 19 SHEET 5 AA112 GLU B 134 SER B 145 -1 N GLU B 134 O LYS B 173 SHEET 6 AA112 VAL B 112 PRO B 127 -1 N LYS B 124 O GLY B 137 SHEET 7 AA112 LYS B 99 LEU B 109 -1 N LEU B 107 O LYS B 114 SHEET 8 AA112 GLN B 86 ASP B 96 -1 N ASN B 88 O THR B 108 SHEET 9 AA112 THR B 50 ASP B 58 -1 N VAL B 55 O TYR B 89 SHEET 10 AA112 SER B 38 ASP B 45 -1 N ASP B 45 O THR B 50 SHEET 11 AA112 ALA B 7 PHE B 11 -1 N TYR B 9 O VAL B 42 SHEET 12 AA112 LYS B 162 LYS B 173 -1 O VAL B 172 N GLN B 10 SHEET 1 AA212 ILE C 62 HIS C 63 0 SHEET 2 AA212 SER C 29 PHE C 35 -1 N LYS C 34 O HIS C 63 SHEET 3 AA212 TYR C 17 HIS C 24 -1 N ALA C 22 O TRP C 31 SHEET 4 AA212 LYS C 162 LYS C 173 -1 O LEU C 166 N SER C 19 SHEET 5 AA212 GLU C 134 SER C 145 -1 N ALA C 140 O ILE C 167 SHEET 6 AA212 VAL C 112 PRO C 127 -1 N LYS C 124 O GLY C 137 SHEET 7 AA212 LYS C 99 LEU C 109 -1 N VAL C 103 O LEU C 118 SHEET 8 AA212 GLN C 86 ASP C 96 -1 N LYS C 94 O VAL C 101 SHEET 9 AA212 THR C 50 ASP C 58 -1 N VAL C 53 O GLY C 91 SHEET 10 AA212 SER C 38 ASP C 45 -1 N ASP C 45 O THR C 50 SHEET 11 AA212 ALA C 7 PHE C 11 -1 N TYR C 9 O VAL C 42 SHEET 12 AA212 LYS C 162 LYS C 173 -1 O VAL C 172 N GLN C 10 SHEET 1 AA312 ILE A 62 HIS A 63 0 SHEET 2 AA312 SER A 29 PHE A 35 -1 N LYS A 34 O HIS A 63 SHEET 3 AA312 TYR A 17 HIS A 24 -1 N ALA A 22 O TRP A 31 SHEET 4 AA312 LYS A 162 LYS A 173 -1 O LEU A 166 N SER A 19 SHEET 5 AA312 GLU A 134 SER A 145 -1 N GLY A 142 O LEU A 165 SHEET 6 AA312 VAL A 112 PRO A 127 -1 N LYS A 119 O VAL A 141 SHEET 7 AA312 LYS A 99 LEU A 109 -1 N VAL A 103 O LEU A 118 SHEET 8 AA312 GLN A 86 ASP A 96 -1 N ASN A 88 O THR A 108 SHEET 9 AA312 THR A 50 ASP A 58 -1 N VAL A 55 O TYR A 89 SHEET 10 AA312 SER A 38 ASP A 45 -1 N ASP A 45 O THR A 50 SHEET 11 AA312 THR A 8 PHE A 11 -1 N TYR A 9 O VAL A 42 SHEET 12 AA312 LYS A 162 LYS A 173 -1 O VAL A 172 N GLN A 10 SHEET 1 AA412 ILE D 62 HIS D 63 0 SHEET 2 AA412 SER D 29 PHE D 35 -1 N LYS D 34 O HIS D 63 SHEET 3 AA412 TYR D 17 HIS D 24 -1 N ALA D 22 O TRP D 31 SHEET 4 AA412 LYS D 162 LYS D 173 -1 O LEU D 166 N SER D 19 SHEET 5 AA412 GLU D 134 SER D 145 -1 N GLU D 134 O LYS D 173 SHEET 6 AA412 VAL D 112 PRO D 127 -1 N LYS D 124 O GLY D 137 SHEET 7 AA412 LYS D 99 LEU D 109 -1 N LEU D 107 O LYS D 114 SHEET 8 AA412 GLN D 86 ASP D 96 -1 N LYS D 94 O VAL D 101 SHEET 9 AA412 THR D 50 ASP D 58 -1 N VAL D 55 O TYR D 89 SHEET 10 AA412 SER D 38 ASP D 45 -1 N ASP D 45 O THR D 50 SHEET 11 AA412 ALA D 7 PHE D 11 -1 N TYR D 9 O VAL D 42 SHEET 12 AA412 LYS D 162 LYS D 173 -1 O VAL D 172 N GLN D 10 SSBOND 1 CYS B 125 CYS B 136 1555 1555 2.16 SSBOND 2 CYS C 125 CYS C 136 1555 1555 2.13 SSBOND 3 CYS A 125 CYS A 136 1555 1555 2.13 SSBOND 4 CYS D 125 CYS D 136 1555 1555 2.07 SITE 1 AC1 12 HIS A 15 HIS B 24 PHE B 25 PHE B 35 SITE 2 AC1 12 THR B 57 CYS B 136 TYR B 153 PHE B 159 SITE 3 AC1 12 ILE B 167 HOH B 301 HOH B 314 HOH B 379 SITE 1 AC2 10 ALA B 76 GLU B 77 PHE B 78 ASP B 80 SITE 2 AC2 10 HIS B 110 GLY B 150 LEU B 151 ASP B 152 SITE 3 AC2 10 TYR B 153 HOH B 400 SITE 1 AC3 15 ALA C 22 HIS C 24 TRP C 31 PHE C 35 SITE 2 AC3 15 VAL C 55 THR C 57 LEU C 69 PHE C 123 SITE 3 AC3 15 CYS C 136 VAL C 138 ALA C 140 ARG C 146 SITE 4 AC3 15 TYR C 153 ILE C 167 HIS D 15 SITE 1 AC4 14 ALA A 22 HIS A 24 TRP A 31 PHE A 35 SITE 2 AC4 14 VAL A 55 THR A 57 LYS A 68 LEU A 69 SITE 3 AC4 14 CYS A 136 TYR A 153 ILE A 167 HOH A 309 SITE 4 AC4 14 HOH A 401 HIS B 15 SITE 1 AC5 13 ALA A 76 HIS C 15 ALA D 22 HIS D 24 SITE 2 AC5 13 TRP D 31 PHE D 35 VAL D 55 THR D 57 SITE 3 AC5 13 LEU D 69 CYS D 136 ARG D 146 TYR D 153 SITE 4 AC5 13 HOH D 343 CRYST1 51.160 101.170 63.490 90.00 97.20 90.00 P 1 21 1 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 0.019547 0.000000 0.002469 0.00000 SCALE2 0.000000 0.009884 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015876 0.00000