HEADER LYASE 12-SEP-17 5YDB TITLE CRYSTAL STRUCTURE OF THE COMPLEX OF TYPE II DEHYDROQUINATE DEHYDRATASE TITLE 2 FROM ACINETOBACTER BAUMANNII WITH DEHYDROQUINIC ACID AT 1.76 ANGSTROM TITLE 3 RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3-DEHYDROQUINATE DEHYDRATASE; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: UNP RESIDUES 3-150; COMPND 5 SYNONYM: 3-DEHYDROQUINASE,TYPE II DHQASE; COMPND 6 EC: 4.2.1.10; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ACINETOBACTER BAUMANNII (STRAIN ATCC 17978 / SOURCE 3 CIP 53.77 / LMG 1025 / NCDC KC755 / 5377); SOURCE 4 ORGANISM_TAXID: 400667; SOURCE 5 STRAIN: ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377; SOURCE 6 GENE: AROQ, A1S_2009; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LYASE EXPDTA X-RAY DIFFRACTION AUTHOR N.IQBAL,P.KAUR,S.SHARMA,T.P.SINGH REVDAT 4 22-NOV-23 5YDB 1 REMARK REVDAT 3 11-JUL-18 5YDB 1 REMARK REVDAT 2 04-JUL-18 5YDB 1 REMARK REVDAT 1 20-SEP-17 5YDB 0 JRNL AUTH N.IQBAL,P.KAUR,S.SHARMA,T.P.SINGH JRNL TITL CRYSTAL STRUCTURE OF THE COMPLEX OF TYPE II DEHYDROQUINATE JRNL TITL 2 DEHYDRATASE FROM ACINETOBACTER BAUMANNII WITH DEHYDROQUINIC JRNL TITL 3 ACID AT 1.76 ANGSTROM RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.76 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.76 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 69.56 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 53283 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) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 2666 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) : 1.76 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.81 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3758 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.48 REMARK 3 BIN R VALUE (WORKING SET) : 0.3690 REMARK 3 BIN FREE R VALUE SET COUNT : 227 REMARK 3 BIN FREE R VALUE : 0.4020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4484 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 56 REMARK 3 SOLVENT ATOMS : 202 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.17 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.40000 REMARK 3 B22 (A**2) : -0.40000 REMARK 3 B33 (A**2) : 1.28000 REMARK 3 B12 (A**2) : -0.20000 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): 0.132 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.133 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.141 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.020 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 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): 4626 ; 0.024 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4520 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6303 ; 2.153 ; 1.960 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10345 ; 1.222 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 576 ; 6.512 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 205 ;36.127 ;24.244 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 755 ;17.450 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ;10.506 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 748 ; 0.154 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5241 ; 0.013 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1064 ; 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): 2316 ; 3.128 ; 3.649 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2315 ; 3.122 ; 3.647 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2888 ; 4.832 ; 5.447 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2889 ; 4.831 ; 5.450 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2310 ; 3.718 ; 4.208 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2306 ; 3.714 ; 4.205 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3412 ; 5.501 ; 6.168 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 19332 ; 9.909 ;34.701 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 19331 ; 9.909 ;34.699 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 : A 3 A 147 REMARK 3 ORIGIN FOR THE GROUP (A): -17.0506 -5.1799 -26.8503 REMARK 3 T TENSOR REMARK 3 T11: 0.0572 T22: 0.0922 REMARK 3 T33: 0.1032 T12: -0.0222 REMARK 3 T13: 0.0247 T23: 0.0320 REMARK 3 L TENSOR REMARK 3 L11: 0.8489 L22: 0.1787 REMARK 3 L33: 0.3222 L12: 0.2811 REMARK 3 L13: 0.1857 L23: 0.1303 REMARK 3 S TENSOR REMARK 3 S11: 0.0865 S12: -0.0766 S13: 0.0195 REMARK 3 S21: 0.0281 S22: -0.0472 S23: 0.0037 REMARK 3 S31: 0.0335 S32: -0.0599 S33: -0.0394 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 : B 3 B 147 REMARK 3 ORIGIN FOR THE GROUP (A): -31.2141 -7.1055 -47.0185 REMARK 3 T TENSOR REMARK 3 T11: 0.0088 T22: 0.1261 REMARK 3 T33: 0.1331 T12: -0.0027 REMARK 3 T13: -0.0230 T23: 0.0550 REMARK 3 L TENSOR REMARK 3 L11: 0.1964 L22: 0.3426 REMARK 3 L33: 1.1050 L12: -0.0728 REMARK 3 L13: 0.0209 L23: -0.1616 REMARK 3 S TENSOR REMARK 3 S11: 0.0377 S12: -0.0062 S13: -0.0756 REMARK 3 S21: 0.0023 S22: 0.0366 S23: 0.0481 REMARK 3 S31: -0.0040 S32: -0.1661 S33: -0.0743 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 : C 3 C 147 REMARK 3 ORIGIN FOR THE GROUP (A): -25.8254 8.9275 -72.6231 REMARK 3 T TENSOR REMARK 3 T11: 0.0506 T22: 0.1347 REMARK 3 T33: 0.0706 T12: 0.0371 REMARK 3 T13: -0.0390 T23: 0.0322 REMARK 3 L TENSOR REMARK 3 L11: 0.7330 L22: 0.7247 REMARK 3 L33: 0.3223 L12: -0.0425 REMARK 3 L13: 0.0251 L23: 0.0699 REMARK 3 S TENSOR REMARK 3 S11: 0.0209 S12: 0.1330 S13: 0.0057 REMARK 3 S21: -0.0335 S22: -0.0298 S23: 0.0073 REMARK 3 S31: -0.0269 S32: -0.0704 S33: 0.0089 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 3 D 147 REMARK 3 ORIGIN FOR THE GROUP (A): -8.9250 26.7006 -71.3570 REMARK 3 T TENSOR REMARK 3 T11: 0.0420 T22: 0.0777 REMARK 3 T33: 0.1827 T12: 0.0001 REMARK 3 T13: 0.0033 T23: 0.1183 REMARK 3 L TENSOR REMARK 3 L11: 1.3787 L22: 0.2598 REMARK 3 L33: 0.3089 L12: 0.3135 REMARK 3 L13: -0.0764 L23: 0.2221 REMARK 3 S TENSOR REMARK 3 S11: -0.0252 S12: 0.2294 S13: 0.3114 REMARK 3 S21: 0.0333 S22: 0.0430 S23: 0.0778 REMARK 3 S31: 0.0444 S32: -0.0172 S33: -0.0178 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 5YDB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-SEP-17. REMARK 100 THE DEPOSITION ID IS D_1300005039. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JUL-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : MASSIF-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 56929 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.760 REMARK 200 RESOLUTION RANGE LOW (A) : 69.560 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.76 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.82 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.700 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: 5B6P REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05M CADMIUM SULFATE HYDRATE, 0.1M REMARK 280 HEPES, PH 7.5, IM SODIUM ACETATE TRIHYDRATE, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 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+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 69.55850 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 40.15962 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 26.52900 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 69.55850 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 40.15962 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 26.52900 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 69.55850 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 40.15962 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 26.52900 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 80.31924 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 53.05800 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 80.31924 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 53.05800 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 80.31924 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 53.05800 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 148 REMARK 465 ASN A 149 REMARK 465 PRO A 150 REMARK 465 SER B 148 REMARK 465 ASN B 149 REMARK 465 PRO B 150 REMARK 465 SER C 148 REMARK 465 ASN C 149 REMARK 465 PRO C 150 REMARK 465 SER D 148 REMARK 465 ASN D 149 REMARK 465 PRO D 150 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 GLU C 41 CD GLU C 41 OE1 0.102 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO A 21 C - N - CD ANGL. DEV. = -20.2 DEGREES REMARK 500 ARG A 113 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ASP C 48 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG C 113 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ASP D 30 CB - CG - OD1 ANGL. DEV. = 9.7 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 ASN A 12 -7.38 77.35 REMARK 500 LYS A 18 -77.00 -112.30 REMARK 500 ARG A 19 82.97 -43.58 REMARK 500 GLU A 20 100.94 53.49 REMARK 500 PRO A 21 40.49 -101.09 REMARK 500 TYR A 24 -126.36 61.82 REMARK 500 ALA A 78 -134.05 55.37 REMARK 500 ARG A 109 -158.65 -111.27 REMARK 500 ASN B 12 -10.37 71.01 REMARK 500 GLU B 22 -5.65 78.49 REMARK 500 TYR B 24 51.41 165.62 REMARK 500 HIS B 26 -67.82 172.23 REMARK 500 ALA B 78 -136.21 58.18 REMARK 500 ARG B 109 -166.97 -107.65 REMARK 500 ASN C 12 -10.73 72.83 REMARK 500 GLU C 20 73.39 41.41 REMARK 500 ALA C 78 -139.65 63.11 REMARK 500 ASN C 105 96.20 -64.05 REMARK 500 ARG C 109 -158.87 -108.39 REMARK 500 ASN D 12 -12.15 79.49 REMARK 500 LYS D 18 -155.74 -78.29 REMARK 500 GLU D 22 -4.47 -58.77 REMARK 500 TYR D 24 84.81 83.25 REMARK 500 ALA D 78 -138.42 56.13 REMARK 500 ARG D 109 -163.31 -110.21 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 A 359 DISTANCE = 5.96 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DQA A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DQA B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA C 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DQA C 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA D 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DQA D 202 DBREF 5YDB A 3 150 UNP A3M692 AROQ_ACIBT 3 150 DBREF 5YDB B 3 150 UNP A3M692 AROQ_ACIBT 3 150 DBREF 5YDB C 3 150 UNP A3M692 AROQ_ACIBT 3 150 DBREF 5YDB D 3 150 UNP A3M692 AROQ_ACIBT 3 150 SEQRES 1 A 148 SER THR ILE LEU VAL ILE HIS GLY PRO ASN LEU ASN LEU SEQRES 2 A 148 LEU GLY LYS ARG GLU PRO GLU VAL TYR GLY HIS LEU THR SEQRES 3 A 148 LEU ASP ASN ILE ASN ARG GLN LEU ILE ALA GLN ALA GLU SEQRES 4 A 148 GLN ALA SER ILE THR LEU ASP THR PHE GLN SER ASN TRP SEQRES 5 A 148 GLU GLY ALA ILE VAL ASP ARG ILE HIS GLN ALA GLN THR SEQRES 6 A 148 GLU GLY VAL LYS LEU ILE ILE ILE ASN PRO ALA ALA LEU SEQRES 7 A 148 THR HIS THR SER VAL ALA LEU ARG ASP ALA LEU LEU GLY SEQRES 8 A 148 VAL ALA ILE PRO PHE ILE GLU VAL HIS LEU SER ASN VAL SEQRES 9 A 148 HIS ALA ARG GLU ALA PHE ARG HIS HIS SER TYR LEU SER SEQRES 10 A 148 ASP LYS ALA ILE GLY VAL ILE CYS GLY LEU GLY ALA LYS SEQRES 11 A 148 GLY TYR SER PHE ALA LEU ASP TYR ALA ILE GLU LYS ILE SEQRES 12 A 148 GLN PRO SER ASN PRO SEQRES 1 B 148 SER THR ILE LEU VAL ILE HIS GLY PRO ASN LEU ASN LEU SEQRES 2 B 148 LEU GLY LYS ARG GLU PRO GLU VAL TYR GLY HIS LEU THR SEQRES 3 B 148 LEU ASP ASN ILE ASN ARG GLN LEU ILE ALA GLN ALA GLU SEQRES 4 B 148 GLN ALA SER ILE THR LEU ASP THR PHE GLN SER ASN TRP SEQRES 5 B 148 GLU GLY ALA ILE VAL ASP ARG ILE HIS GLN ALA GLN THR SEQRES 6 B 148 GLU GLY VAL LYS LEU ILE ILE ILE ASN PRO ALA ALA LEU SEQRES 7 B 148 THR HIS THR SER VAL ALA LEU ARG ASP ALA LEU LEU GLY SEQRES 8 B 148 VAL ALA ILE PRO PHE ILE GLU VAL HIS LEU SER ASN VAL SEQRES 9 B 148 HIS ALA ARG GLU ALA PHE ARG HIS HIS SER TYR LEU SER SEQRES 10 B 148 ASP LYS ALA ILE GLY VAL ILE CYS GLY LEU GLY ALA LYS SEQRES 11 B 148 GLY TYR SER PHE ALA LEU ASP TYR ALA ILE GLU LYS ILE SEQRES 12 B 148 GLN PRO SER ASN PRO SEQRES 1 C 148 SER THR ILE LEU VAL ILE HIS GLY PRO ASN LEU ASN LEU SEQRES 2 C 148 LEU GLY LYS ARG GLU PRO GLU VAL TYR GLY HIS LEU THR SEQRES 3 C 148 LEU ASP ASN ILE ASN ARG GLN LEU ILE ALA GLN ALA GLU SEQRES 4 C 148 GLN ALA SER ILE THR LEU ASP THR PHE GLN SER ASN TRP SEQRES 5 C 148 GLU GLY ALA ILE VAL ASP ARG ILE HIS GLN ALA GLN THR SEQRES 6 C 148 GLU GLY VAL LYS LEU ILE ILE ILE ASN PRO ALA ALA LEU SEQRES 7 C 148 THR HIS THR SER VAL ALA LEU ARG ASP ALA LEU LEU GLY SEQRES 8 C 148 VAL ALA ILE PRO PHE ILE GLU VAL HIS LEU SER ASN VAL SEQRES 9 C 148 HIS ALA ARG GLU ALA PHE ARG HIS HIS SER TYR LEU SER SEQRES 10 C 148 ASP LYS ALA ILE GLY VAL ILE CYS GLY LEU GLY ALA LYS SEQRES 11 C 148 GLY TYR SER PHE ALA LEU ASP TYR ALA ILE GLU LYS ILE SEQRES 12 C 148 GLN PRO SER ASN PRO SEQRES 1 D 148 SER THR ILE LEU VAL ILE HIS GLY PRO ASN LEU ASN LEU SEQRES 2 D 148 LEU GLY LYS ARG GLU PRO GLU VAL TYR GLY HIS LEU THR SEQRES 3 D 148 LEU ASP ASN ILE ASN ARG GLN LEU ILE ALA GLN ALA GLU SEQRES 4 D 148 GLN ALA SER ILE THR LEU ASP THR PHE GLN SER ASN TRP SEQRES 5 D 148 GLU GLY ALA ILE VAL ASP ARG ILE HIS GLN ALA GLN THR SEQRES 6 D 148 GLU GLY VAL LYS LEU ILE ILE ILE ASN PRO ALA ALA LEU SEQRES 7 D 148 THR HIS THR SER VAL ALA LEU ARG ASP ALA LEU LEU GLY SEQRES 8 D 148 VAL ALA ILE PRO PHE ILE GLU VAL HIS LEU SER ASN VAL SEQRES 9 D 148 HIS ALA ARG GLU ALA PHE ARG HIS HIS SER TYR LEU SER SEQRES 10 D 148 ASP LYS ALA ILE GLY VAL ILE CYS GLY LEU GLY ALA LYS SEQRES 11 D 148 GLY TYR SER PHE ALA LEU ASP TYR ALA ILE GLU LYS ILE SEQRES 12 D 148 GLN PRO SER ASN PRO HET NA A 201 1 HET DQA A 202 13 HET NA B 201 1 HET DQA B 202 13 HET NA C 201 1 HET DQA C 202 13 HET NA D 201 1 HET DQA D 202 13 HETNAM NA SODIUM ION HETNAM DQA 1,3,4-TRIHYDROXY-5-OXO-CYCLOHEXANECARBOXYLIC ACID HETSYN DQA 3-DEHYDROQUINIC ACID FORMUL 5 NA 4(NA 1+) FORMUL 6 DQA 4(C7 H10 O6) FORMUL 13 HOH *202(H2 O) HELIX 1 AA1 ASN A 12 LEU A 16 5 5 HELIX 2 AA2 THR A 28 ALA A 43 1 16 HELIX 3 AA3 TRP A 54 GLU A 68 1 15 HELIX 4 AA4 PRO A 77 THR A 83 5 7 HELIX 5 AA5 SER A 84 ALA A 95 1 12 HELIX 6 AA6 ASN A 105 ARG A 109 5 5 HELIX 7 AA7 GLU A 110 HIS A 115 5 6 HELIX 8 AA8 LEU A 118 ALA A 122 5 5 HELIX 9 AA9 ALA A 131 GLN A 146 1 16 HELIX 10 AB1 ASN B 12 LEU B 16 5 5 HELIX 11 AB2 THR B 28 ALA B 43 1 16 HELIX 12 AB3 TRP B 54 GLY B 69 1 16 HELIX 13 AB4 PRO B 77 THR B 83 5 7 HELIX 14 AB5 SER B 84 ALA B 95 1 12 HELIX 15 AB6 ASN B 105 ARG B 109 5 5 HELIX 16 AB7 GLU B 110 HIS B 115 5 6 HELIX 17 AB8 LEU B 118 ALA B 122 5 5 HELIX 18 AB9 ALA B 131 GLN B 146 1 16 HELIX 19 AC1 ASN C 12 LEU C 16 5 5 HELIX 20 AC2 GLU C 20 GLY C 25 1 6 HELIX 21 AC3 THR C 28 ALA C 43 1 16 HELIX 22 AC4 TRP C 54 GLU C 68 1 15 HELIX 23 AC5 PRO C 77 THR C 83 5 7 HELIX 24 AC6 SER C 84 ALA C 95 1 12 HELIX 25 AC7 ASN C 105 ARG C 109 5 5 HELIX 26 AC8 GLU C 110 HIS C 115 5 6 HELIX 27 AC9 LEU C 118 ALA C 122 5 5 HELIX 28 AD1 ALA C 131 GLN C 146 1 16 HELIX 29 AD2 ASN D 12 LEU D 16 5 5 HELIX 30 AD3 GLU D 20 TYR D 24 5 5 HELIX 31 AD4 THR D 28 ALA D 43 1 16 HELIX 32 AD5 TRP D 54 GLY D 69 1 16 HELIX 33 AD6 PRO D 77 THR D 83 5 7 HELIX 34 AD7 SER D 84 VAL D 94 1 11 HELIX 35 AD8 ASN D 105 ARG D 109 5 5 HELIX 36 AD9 GLU D 110 HIS D 115 5 6 HELIX 37 AE1 LEU D 118 ALA D 122 5 5 HELIX 38 AE2 ALA D 131 GLN D 146 1 16 SHEET 1 AA110 LEU A 47 GLN A 51 0 SHEET 2 AA110 ILE A 5 HIS A 9 1 N ILE A 5 O ASP A 48 SHEET 3 AA110 LEU A 72 ASN A 76 1 O ASN A 76 N ILE A 8 SHEET 4 AA110 PHE A 98 HIS A 102 1 O ILE A 99 N ILE A 75 SHEET 5 AA110 GLY A 124 CYS A 127 1 O ILE A 126 N HIS A 102 SHEET 6 AA110 VAL B 125 CYS B 127 -1 O VAL B 125 N CYS A 127 SHEET 7 AA110 PHE B 98 HIS B 102 1 N HIS B 102 O ILE B 126 SHEET 8 AA110 LEU B 72 ASN B 76 1 N ILE B 75 O ILE B 99 SHEET 9 AA110 ILE B 5 HIS B 9 1 N ILE B 8 O ILE B 74 SHEET 10 AA110 LEU B 47 GLN B 51 1 O PHE B 50 N HIS B 9 SHEET 1 AA210 LEU C 47 GLN C 51 0 SHEET 2 AA210 ILE C 5 HIS C 9 1 N VAL C 7 O ASP C 48 SHEET 3 AA210 LEU C 72 ASN C 76 1 O ASN C 76 N ILE C 8 SHEET 4 AA210 PHE C 98 HIS C 102 1 O ILE C 99 N ILE C 75 SHEET 5 AA210 GLY C 124 CYS C 127 1 O ILE C 126 N HIS C 102 SHEET 6 AA210 GLY D 124 CYS D 127 -1 O CYS D 127 N VAL C 125 SHEET 7 AA210 PHE D 98 HIS D 102 1 N HIS D 102 O ILE D 126 SHEET 8 AA210 LEU D 72 ASN D 76 1 N ILE D 75 O ILE D 99 SHEET 9 AA210 ILE D 5 HIS D 9 1 N ILE D 8 O ILE D 74 SHEET 10 AA210 LEU D 47 GLN D 51 1 O PHE D 50 N HIS D 9 CISPEP 1 ARG D 19 GLU D 20 0 15.44 CISPEP 2 TYR D 24 GLY D 25 0 24.35 SITE 1 AC1 2 HIS A 107 CYS A 127 SITE 1 AC2 10 ASN A 76 ALA A 78 ALA A 79 HIS A 82 SITE 2 AC2 10 ASP A 89 HIS A 102 LEU A 103 SER A 104 SITE 3 AC2 10 ARG A 113 HOH A 310 SITE 1 AC3 2 HIS B 107 CYS B 127 SITE 1 AC4 10 ASN B 76 ALA B 78 ALA B 79 HIS B 82 SITE 2 AC4 10 HIS B 102 LEU B 103 SER B 104 ARG B 113 SITE 3 AC4 10 HOH B 324 ASP D 89 SITE 1 AC5 2 HIS C 107 CYS C 127 SITE 1 AC6 11 ASP B 89 ASN C 76 ALA C 78 ALA C 79 SITE 2 AC6 11 HIS C 82 HIS C 102 LEU C 103 SER C 104 SITE 3 AC6 11 VAL C 106 ARG C 113 HOH C 309 SITE 1 AC7 2 HIS D 107 CYS D 127 SITE 1 AC8 11 ASP C 89 ASN D 76 ALA D 78 ALA D 79 SITE 2 AC8 11 HIS D 82 HIS D 102 LEU D 103 SER D 104 SITE 3 AC8 11 ARG D 109 ARG D 113 HOH D 313 CRYST1 139.117 139.117 79.587 90.00 90.00 120.00 H 3 36 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 0.007188 0.004150 0.000000 0.00000 SCALE2 0.000000 0.008300 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012565 0.00000