HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 24-JUN-03 1PUG TITLE STRUCTURE OF E. COLI YBAB COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL UPF0133 PROTEIN YBAB; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: YBAB; HYPOTHETICAL PROTEIN YBAB; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: YBAB; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: B834 DE3; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET T7 KEYWDS NYSGXRC T5, UNKNOWN FUNCTION, PSI, PROTEIN STRUCTURE INITIATIVE, NEW KEYWDS 2 YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS, STRUCTURAL KEYWDS 3 GENOMICS EXPDTA X-RAY DIFFRACTION AUTHOR R.KNIEWEL,J.BUGLINO,T.CHADNA,C.D.LIMA,S.K.BURLEY,NEW YORK SGX AUTHOR 2 RESEARCH CENTER FOR STRUCTURAL GENOMICS (NYSGXRC) REVDAT 6 14-FEB-24 1PUG 1 REMARK REVDAT 5 03-FEB-21 1PUG 1 AUTHOR REVDAT 4 25-OCT-17 1PUG 1 REMARK REVDAT 3 24-FEB-09 1PUG 1 VERSN REVDAT 2 25-JAN-05 1PUG 1 AUTHOR KEYWDS REMARK REVDAT 1 08-JUL-03 1PUG 0 JRNL AUTH R.KNIEWEL,J.BUGLINO,T.CHADNA,C.D.LIMA JRNL TITL STRUCTURE OF E. COLI YBAB JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 22865 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) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.284 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1177 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1605 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2370 REMARK 3 BIN FREE R VALUE SET COUNT : 92 REMARK 3 BIN FREE R VALUE : 0.2980 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2492 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 163 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 63.38 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.41000 REMARK 3 B22 (A**2) : -3.67000 REMARK 3 B33 (A**2) : 1.26000 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): 0.221 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.217 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.136 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.202 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.939 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.902 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2502 ; 0.032 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2303 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3345 ; 2.407 ; 1.975 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5413 ; 1.187 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 319 ; 8.222 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 381 ; 0.142 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2783 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 405 ; 0.014 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 624 ; 0.270 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2754 ; 0.267 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 1644 ; 0.104 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 125 ; 0.230 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 19 ; 0.324 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 72 ; 0.369 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 24 ; 0.414 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1599 ; 1.776 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2551 ; 3.134 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 903 ; 3.966 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 794 ; 6.845 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 1PUG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-JUN-03. REMARK 100 THE DEPOSITION ID IS D_1000019575. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-MAY-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 31-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9798 REMARK 200 MONOCHROMATOR : SAGITALLY FOCUSED SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36898 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -0.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.5 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: SIR REMARK 200 SOFTWARE USED: SOLVE, RESOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.9M AMMONIUM SULFATE 0.1MSODIUM HEPES REMARK 280 PH 7.5 5% ETHYLENE GLYCOL, VAPOR DIFFUSION, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 31.93300 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.11800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.93300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.11800 REMARK 290 SMTRY3 4 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 300 REMARK: APPARENT DIMER (A,B) AND (C,D) ALSO BY GEL FILTRATION 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: 1680 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10440 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 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 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: 1720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 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 MET A 1 REMARK 465 PHE A 2 REMARK 465 GLY A 3 REMARK 465 LYS A 4 REMARK 465 GLY A 5 REMARK 465 GLY A 6 REMARK 465 LEU A 7 REMARK 465 GLY A 8 REMARK 465 ASN A 9 REMARK 465 LEU A 10 REMARK 465 PHE A 105 REMARK 465 LYS A 106 REMARK 465 MET A 107 REMARK 465 PRO A 108 REMARK 465 PHE A 109 REMARK 465 MET B 1 REMARK 465 PHE B 2 REMARK 465 GLY B 3 REMARK 465 LYS B 4 REMARK 465 GLY B 5 REMARK 465 GLY B 6 REMARK 465 LEU B 7 REMARK 465 GLY B 8 REMARK 465 ASN B 9 REMARK 465 LEU B 10 REMARK 465 MET B 11 REMARK 465 LYS B 12 REMARK 465 GLN B 13 REMARK 465 ALA B 14 REMARK 465 GLN B 15 REMARK 465 GLN B 16 REMARK 465 MET B 17 REMARK 465 MET B 92 REMARK 465 ALA B 93 REMARK 465 SER B 94 REMARK 465 VAL B 95 REMARK 465 SER B 96 REMARK 465 SER B 97 REMARK 465 GLY B 98 REMARK 465 MET B 99 REMARK 465 GLN B 100 REMARK 465 LEU B 101 REMARK 465 PRO B 102 REMARK 465 PRO B 103 REMARK 465 GLY B 104 REMARK 465 PHE B 105 REMARK 465 LYS B 106 REMARK 465 MET B 107 REMARK 465 PRO B 108 REMARK 465 PHE B 109 REMARK 465 MET C 1 REMARK 465 PHE C 2 REMARK 465 GLY C 3 REMARK 465 LYS C 4 REMARK 465 GLY C 5 REMARK 465 GLY C 6 REMARK 465 LEU C 7 REMARK 465 GLY C 8 REMARK 465 ASN C 9 REMARK 465 LEU C 10 REMARK 465 MET C 11 REMARK 465 LYS C 12 REMARK 465 GLN C 13 REMARK 465 ALA C 14 REMARK 465 GLN C 15 REMARK 465 SER C 96 REMARK 465 SER C 97 REMARK 465 GLY C 98 REMARK 465 MET C 99 REMARK 465 GLN C 100 REMARK 465 LEU C 101 REMARK 465 PRO C 102 REMARK 465 PRO C 103 REMARK 465 GLY C 104 REMARK 465 PHE C 105 REMARK 465 LYS C 106 REMARK 465 MET C 107 REMARK 465 PRO C 108 REMARK 465 PHE C 109 REMARK 465 MET D 1 REMARK 465 PHE D 2 REMARK 465 GLY D 3 REMARK 465 LYS D 4 REMARK 465 GLY D 5 REMARK 465 GLY D 6 REMARK 465 LEU D 7 REMARK 465 GLY D 8 REMARK 465 ASN D 9 REMARK 465 LEU D 10 REMARK 465 MET D 11 REMARK 465 LYS D 12 REMARK 465 GLN D 13 REMARK 465 ALA D 14 REMARK 465 GLN D 15 REMARK 465 GLN D 16 REMARK 465 MET D 17 REMARK 465 GLN D 18 REMARK 465 GLU D 19 REMARK 465 LYS D 20 REMARK 465 SER D 96 REMARK 465 SER D 97 REMARK 465 GLY D 98 REMARK 465 MET D 99 REMARK 465 GLN D 100 REMARK 465 LEU D 101 REMARK 465 PRO D 102 REMARK 465 PRO D 103 REMARK 465 GLY D 104 REMARK 465 PHE D 105 REMARK 465 LYS D 106 REMARK 465 MET D 107 REMARK 465 PRO D 108 REMARK 465 PHE D 109 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 CB HIS B 50 O HOH B 141 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH B 135 O HOH B 135 2555 1.09 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 ARG A 54 CB ARG A 54 CG -0.187 REMARK 500 GLU A 90 CD GLU A 90 OE1 0.069 REMARK 500 GLU A 90 CD GLU A 90 OE2 0.079 REMARK 500 GLU B 67 CD GLU B 67 OE2 0.105 REMARK 500 GLU C 32 CD GLU C 32 OE2 -0.083 REMARK 500 SER C 37 CB SER C 37 OG -0.120 REMARK 500 ARG C 53 CD ARG C 53 NE -0.104 REMARK 500 MET C 68 CG MET C 68 SD -0.159 REMARK 500 GLY D 38 N GLY D 38 CA 0.109 REMARK 500 GLU D 67 CD GLU D 67 OE1 0.097 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 79 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP B 65 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 MET B 68 CG - SD - CE ANGL. DEV. = -9.6 DEGREES REMARK 500 GLY C 38 N - CA - C ANGL. DEV. = -17.7 DEGREES REMARK 500 GLY C 38 O - C - N ANGL. DEV. = -12.2 DEGREES REMARK 500 ALA C 39 C - N - CA ANGL. DEV. = -25.9 DEGREES REMARK 500 ARG C 53 CD - NE - CZ ANGL. DEV. = 11.0 DEGREES REMARK 500 ARG C 53 NE - CZ - NH1 ANGL. DEV. = 7.8 DEGREES REMARK 500 ARG C 53 NE - CZ - NH2 ANGL. DEV. = -7.8 DEGREES REMARK 500 ASP C 58 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP C 64 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP C 71 CB - CG - OD2 ANGL. DEV. = 6.7 DEGREES REMARK 500 ASP C 79 CB - CG - OD2 ANGL. DEV. = 6.0 DEGREES REMARK 500 ARG C 82 NE - CZ - NH2 ANGL. DEV. = -5.2 DEGREES REMARK 500 SER D 37 O - C - N ANGL. DEV. = -15.1 DEGREES REMARK 500 GLY D 38 C - N - CA ANGL. DEV. = -27.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLN A 13 -7.19 -148.84 REMARK 500 GLN A 16 25.49 -75.49 REMARK 500 ALA A 39 26.25 44.39 REMARK 500 GLU A 63 -85.10 -45.43 REMARK 500 ASP A 65 89.75 42.19 REMARK 500 LYS B 20 26.34 -142.15 REMARK 500 LYS B 23 76.56 -113.79 REMARK 500 MET B 24 -35.04 -162.69 REMARK 500 HIS B 50 14.01 54.97 REMARK 500 GLU B 63 -77.87 -36.73 REMARK 500 ASP B 65 63.59 -102.85 REMARK 500 GLU B 86 -32.35 -39.99 REMARK 500 GLU C 63 -83.99 -28.55 REMARK 500 ASP C 64 28.07 -141.08 REMARK 500 GLU C 90 23.30 -73.29 REMARK 500 ALA D 29 -39.06 -38.39 REMARK 500 SER D 37 -24.38 -148.50 REMARK 500 THR D 87 -74.06 -45.04 REMARK 500 GLU D 90 -51.74 -168.18 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 MET A 11 LYS A 12 147.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: NYSGXRC-T5 RELATED DB: TARGETDB DBREF 1PUG A 1 109 UNP P0A8B5 YBAB_ECOLI 1 109 DBREF 1PUG B 1 109 UNP P0A8B5 YBAB_ECOLI 1 109 DBREF 1PUG C 1 109 UNP P0A8B5 YBAB_ECOLI 1 109 DBREF 1PUG D 1 109 UNP P0A8B5 YBAB_ECOLI 1 109 SEQRES 1 A 109 MET PHE GLY LYS GLY GLY LEU GLY ASN LEU MET LYS GLN SEQRES 2 A 109 ALA GLN GLN MET GLN GLU LYS MET GLN LYS MET GLN GLU SEQRES 3 A 109 GLU ILE ALA GLN LEU GLU VAL THR GLY GLU SER GLY ALA SEQRES 4 A 109 GLY LEU VAL LYS VAL THR ILE ASN GLY ALA HIS ASN CYS SEQRES 5 A 109 ARG ARG VAL GLU ILE ASP PRO SER LEU LEU GLU ASP ASP SEQRES 6 A 109 LYS GLU MET LEU GLU ASP LEU VAL ALA ALA ALA PHE ASN SEQRES 7 A 109 ASP ALA ALA ARG ARG ILE GLU GLU THR GLN LYS GLU LYS SEQRES 8 A 109 MET ALA SER VAL SER SER GLY MET GLN LEU PRO PRO GLY SEQRES 9 A 109 PHE LYS MET PRO PHE SEQRES 1 B 109 MET PHE GLY LYS GLY GLY LEU GLY ASN LEU MET LYS GLN SEQRES 2 B 109 ALA GLN GLN MET GLN GLU LYS MET GLN LYS MET GLN GLU SEQRES 3 B 109 GLU ILE ALA GLN LEU GLU VAL THR GLY GLU SER GLY ALA SEQRES 4 B 109 GLY LEU VAL LYS VAL THR ILE ASN GLY ALA HIS ASN CYS SEQRES 5 B 109 ARG ARG VAL GLU ILE ASP PRO SER LEU LEU GLU ASP ASP SEQRES 6 B 109 LYS GLU MET LEU GLU ASP LEU VAL ALA ALA ALA PHE ASN SEQRES 7 B 109 ASP ALA ALA ARG ARG ILE GLU GLU THR GLN LYS GLU LYS SEQRES 8 B 109 MET ALA SER VAL SER SER GLY MET GLN LEU PRO PRO GLY SEQRES 9 B 109 PHE LYS MET PRO PHE SEQRES 1 C 109 MET PHE GLY LYS GLY GLY LEU GLY ASN LEU MET LYS GLN SEQRES 2 C 109 ALA GLN GLN MET GLN GLU LYS MET GLN LYS MET GLN GLU SEQRES 3 C 109 GLU ILE ALA GLN LEU GLU VAL THR GLY GLU SER GLY ALA SEQRES 4 C 109 GLY LEU VAL LYS VAL THR ILE ASN GLY ALA HIS ASN CYS SEQRES 5 C 109 ARG ARG VAL GLU ILE ASP PRO SER LEU LEU GLU ASP ASP SEQRES 6 C 109 LYS GLU MET LEU GLU ASP LEU VAL ALA ALA ALA PHE ASN SEQRES 7 C 109 ASP ALA ALA ARG ARG ILE GLU GLU THR GLN LYS GLU LYS SEQRES 8 C 109 MET ALA SER VAL SER SER GLY MET GLN LEU PRO PRO GLY SEQRES 9 C 109 PHE LYS MET PRO PHE SEQRES 1 D 109 MET PHE GLY LYS GLY GLY LEU GLY ASN LEU MET LYS GLN SEQRES 2 D 109 ALA GLN GLN MET GLN GLU LYS MET GLN LYS MET GLN GLU SEQRES 3 D 109 GLU ILE ALA GLN LEU GLU VAL THR GLY GLU SER GLY ALA SEQRES 4 D 109 GLY LEU VAL LYS VAL THR ILE ASN GLY ALA HIS ASN CYS SEQRES 5 D 109 ARG ARG VAL GLU ILE ASP PRO SER LEU LEU GLU ASP ASP SEQRES 6 D 109 LYS GLU MET LEU GLU ASP LEU VAL ALA ALA ALA PHE ASN SEQRES 7 D 109 ASP ALA ALA ARG ARG ILE GLU GLU THR GLN LYS GLU LYS SEQRES 8 D 109 MET ALA SER VAL SER SER GLY MET GLN LEU PRO PRO GLY SEQRES 9 D 109 PHE LYS MET PRO PHE FORMUL 5 HOH *163(H2 O) HELIX 1 1 MET A 17 GLN A 30 1 14 HELIX 2 2 GLY A 38 GLY A 40 5 3 HELIX 3 3 PRO A 59 LEU A 62 5 4 HELIX 4 4 ASP A 65 GLY A 98 1 34 HELIX 5 5 MET B 24 LEU B 31 1 8 HELIX 6 6 GLY B 38 GLY B 40 5 3 HELIX 7 7 PRO B 59 LEU B 62 5 4 HELIX 8 8 ASP B 65 LYS B 91 1 27 HELIX 9 9 GLN C 16 LEU C 31 1 16 HELIX 10 10 PRO C 59 LEU C 62 5 4 HELIX 11 11 ASP C 65 GLU C 90 1 26 HELIX 12 12 GLN D 22 LEU D 31 1 10 HELIX 13 13 PRO D 59 GLU D 63 5 5 HELIX 14 14 ASP D 65 MET D 92 1 28 SHEET 1 A 3 GLU A 32 SER A 37 0 SHEET 2 A 3 VAL A 42 ASN A 47 -1 O VAL A 44 N GLY A 35 SHEET 3 A 3 CYS A 52 ILE A 57 -1 O ARG A 54 N THR A 45 SHEET 1 B 3 GLU B 32 SER B 37 0 SHEET 2 B 3 VAL B 42 ASN B 47 -1 O VAL B 44 N GLY B 35 SHEET 3 B 3 CYS B 52 ILE B 57 -1 O ARG B 54 N THR B 45 SHEET 1 C 3 GLU C 32 SER C 37 0 SHEET 2 C 3 VAL C 42 ASN C 47 -1 O ILE C 46 N VAL C 33 SHEET 3 C 3 CYS C 52 ILE C 57 -1 O GLU C 56 N LYS C 43 SHEET 1 D 3 GLU D 32 GLU D 36 0 SHEET 2 D 3 VAL D 42 ASN D 47 -1 O VAL D 44 N GLY D 35 SHEET 3 D 3 CYS D 52 ILE D 57 -1 O ARG D 54 N THR D 45 CRYST1 63.866 84.236 86.636 90.00 90.00 90.00 P 21 21 2 16 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 0.015658 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011871 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011543 0.00000