HEADER TRANSFERASE 07-MAR-05 2BLN TITLE N-TERMINAL FORMYLTRANSFERASE DOMAIN OF ARNA IN COMPLEX WITH N-5- TITLE 2 FORMYLTETRAHYDROFOLATE AND UMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN YFBG; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: FORMYLTRANSFERASE DOMAIN, RESIDUES 1-305; COMPND 5 SYNONYM: UDP-D-GLUCURONATE DEHYDROGENASE ARNA; COMPND 6 EC: 2.1.1.2; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 STRAIN: W3310; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET24B KEYWDS TRANSFERASE, FORMYLTRANSFERASE, L-ARA4N BIOSYNTHESIS, KEYWDS 2 METHYLTRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR G.J.WILLIAMS,S.D.BREAZEALE,C.R.H.RAETZ,J.H.NAISMITH REVDAT 4 08-MAY-24 2BLN 1 REMARK REVDAT 3 24-FEB-09 2BLN 1 VERSN REVDAT 2 16-JUN-05 2BLN 1 JRNL REVDAT 1 08-APR-05 2BLN 0 JRNL AUTH G.J.WILLIAMS,S.D.BREAZEALE,C.R.H.RAETZ,J.H.NAISMITH JRNL TITL STRUCTURE AND FUNCTION OF BOTH DOMAINS OF ARNA, A DUAL JRNL TITL 2 FUNCTION DECARBOXYLASE AND A FORMYLTRANSFERASE, INVOLVED IN JRNL TITL 3 4-AMINO-4-DEOXY-L-ARABINOSE BIOSYNTHESIS. JRNL REF J.BIOL.CHEM. V. 280 23000 2005 JRNL REFN ISSN 0021-9258 JRNL PMID 15809294 JRNL DOI 10.1074/JBC.M501534200 REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0007 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) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.70 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 172334 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) : 0.136 REMARK 3 R VALUE (WORKING SET) : 0.135 REMARK 3 FREE R VALUE : 0.158 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 9117 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) : 1.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.23 REMARK 3 REFLECTION IN BIN (WORKING SET) : 12310 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1470 REMARK 3 BIN FREE R VALUE SET COUNT : 668 REMARK 3 BIN FREE R VALUE : 0.1820 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4586 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 118 REMARK 3 SOLVENT ATOMS : 648 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 5.94 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.48000 REMARK 3 B22 (A**2) : 0.26000 REMARK 3 B33 (A**2) : 0.22000 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): 0.035 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.034 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.018 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.839 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.972 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.966 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4885 ; 0.019 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 4453 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6658 ; 1.870 ; 1.971 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10256 ; 2.186 ; 3.002 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 592 ; 7.926 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 212 ;36.012 ;23.208 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 758 ;11.427 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 34 ;16.543 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 745 ; 0.308 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5424 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 984 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1014 ; 0.223 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 4661 ; 0.202 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2467 ; 0.191 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2912 ; 0.096 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 414 ; 0.157 ; 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): 23 ; 0.260 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 112 ; 0.270 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 37 ; 0.130 ; 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): 3735 ; 1.901 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4811 ; 2.193 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2179 ; 3.250 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1847 ; 4.186 ; 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 : 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 1 A 83 REMARK 3 ORIGIN FOR THE GROUP (A): 15.5810 55.4450 12.5660 REMARK 3 T TENSOR REMARK 3 T11: 0.0082 T22: -0.0072 REMARK 3 T33: -0.0460 T12: 0.0080 REMARK 3 T13: 0.0040 T23: -0.0070 REMARK 3 L TENSOR REMARK 3 L11: 0.8281 L22: 0.6371 REMARK 3 L33: 1.0757 L12: 0.0521 REMARK 3 L13: -0.0717 L23: -0.0916 REMARK 3 S TENSOR REMARK 3 S11: -0.0053 S12: -0.0190 S13: 0.0074 REMARK 3 S21: 0.0237 S22: 0.0038 S23: 0.0049 REMARK 3 S31: -0.0516 S32: 0.0164 S33: 0.0015 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 203 A 300 REMARK 3 ORIGIN FOR THE GROUP (A): 53.7460 44.9190 2.4280 REMARK 3 T TENSOR REMARK 3 T11: 0.0076 T22: 0.0029 REMARK 3 T33: -0.0075 T12: 0.0009 REMARK 3 T13: -0.0019 T23: -0.0217 REMARK 3 L TENSOR REMARK 3 L11: 0.8655 L22: 0.6523 REMARK 3 L33: 0.9756 L12: -0.0192 REMARK 3 L13: 0.1607 L23: 0.2986 REMARK 3 S TENSOR REMARK 3 S11: 0.0346 S12: 0.0626 S13: -0.0972 REMARK 3 S21: 0.0127 S22: 0.0365 S23: -0.0390 REMARK 3 S31: 0.0225 S32: 0.0336 S33: -0.0712 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 : B 1 B 83 REMARK 3 ORIGIN FOR THE GROUP (A): 7.7110 15.2530 28.2110 REMARK 3 T TENSOR REMARK 3 T11: 0.0067 T22: -0.0202 REMARK 3 T33: -0.0388 T12: 0.0019 REMARK 3 T13: 0.0085 T23: 0.0085 REMARK 3 L TENSOR REMARK 3 L11: 0.9117 L22: 0.9760 REMARK 3 L33: 0.6224 L12: 0.1141 REMARK 3 L13: 0.0108 L23: -0.0767 REMARK 3 S TENSOR REMARK 3 S11: -0.0026 S12: -0.0304 S13: -0.0794 REMARK 3 S21: 0.0052 S22: 0.0000 S23: -0.0028 REMARK 3 S31: 0.0425 S32: -0.0029 S33: 0.0027 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 : B 203 B 300 REMARK 3 ORIGIN FOR THE GROUP (A): 45.7410 17.4040 13.2640 REMARK 3 T TENSOR REMARK 3 T11: 0.0073 T22: -0.0092 REMARK 3 T33: -0.0437 T12: -0.0009 REMARK 3 T13: -0.0030 T23: -0.0002 REMARK 3 L TENSOR REMARK 3 L11: 0.7360 L22: 0.5509 REMARK 3 L33: 0.7470 L12: -0.0279 REMARK 3 L13: -0.1791 L23: -0.1611 REMARK 3 S TENSOR REMARK 3 S11: 0.0179 S12: 0.0592 S13: -0.0111 REMARK 3 S21: -0.0356 S22: -0.0142 S23: 0.0153 REMARK 3 S31: 0.0278 S32: 0.0124 S33: -0.0037 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 : 1.20 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. A LOOP CONTAINING RESIDUES N35-A40 IS MISSING IN THE REMARK 3 STRUCTURE. THE C-TERMINAL RESIDUE N305 IS MISSING IN THE REMARK 3 STRUCTURE REMARK 4 REMARK 4 2BLN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-MAR-05. REMARK 100 THE DEPOSITION ID IS D_1290023158. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-NOV-03 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.933 REMARK 200 MONOCHROMATOR : DIAMOND (111), GE(220) REMARK 200 OPTICS : TOROIDAL MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 183672 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 27.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.25 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : 0.30000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M AMMONIUM ACETATE, 0.1 M BIS-TRIS REMARK 280 PH 5.5, 17 % PEG 10000, PH 5.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 33.58800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.94250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.97850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.94250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.58800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 44.97850 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 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ASN A 35 REMARK 465 PRO A 36 REMARK 465 GLY A 37 REMARK 465 GLU A 38 REMARK 465 LYS A 39 REMARK 465 ALA A 40 REMARK 465 ASN A 305 REMARK 465 ASN B 35 REMARK 465 PRO B 36 REMARK 465 GLY B 37 REMARK 465 GLU B 38 REMARK 465 LYS B 39 REMARK 465 ALA B 40 REMARK 465 ASN B 305 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 OG SER A 27 O HOH A 2028 1.91 REMARK 500 OE2 GLU B 17 NH2 ARG B 52 2.12 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 CYS B 197 CB CYS B 197 SG -0.142 REMARK 500 CYS B 197 CB CYS B 197 SG -0.197 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 222 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG A 222 NE - CZ - NH2 ANGL. DEV. = -4.9 DEGREES REMARK 500 ARG B 222 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 ARG B 222 NE - CZ - NH2 ANGL. DEV. = -3.5 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 HIS A 9 -160.78 62.26 REMARK 500 THR A 128 -156.90 -148.43 REMARK 500 ILE A 185 73.57 -174.87 REMARK 500 HIS B 9 -162.23 63.22 REMARK 500 THR B 128 -157.14 -150.06 REMARK 500 HIS B 250 -15.79 37.41 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 B2021 DISTANCE = 6.07 ANGSTROMS REMARK 525 HOH B2051 DISTANCE = 6.08 ANGSTROMS REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A1307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B1307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FON A1305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE U5P A1306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FON B1305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE U5P B1306 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1U9J RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E. COLI ARNA (PMRI) DECARBOXYLASEDOMAIN REMARK 900 RELATED ID: 2BLL RELATED DB: PDB REMARK 900 APO-STRUCTURE OF THE C-TERMINAL DECARBOXYLASE DOMAIN OF ARNA DBREF 2BLN A 1 305 UNP P77398 YFBG_ECOLI 1 305 DBREF 2BLN B 1 305 UNP P77398 YFBG_ECOLI 1 305 SEQRES 1 A 305 MET LYS THR VAL VAL PHE ALA TYR HIS ASP MET GLY CYS SEQRES 2 A 305 LEU GLY ILE GLU ALA LEU LEU ALA ALA GLY TYR GLU ILE SEQRES 3 A 305 SER ALA ILE PHE THR HIS THR ASP ASN PRO GLY GLU LYS SEQRES 4 A 305 ALA PHE TYR GLY SER VAL ALA ARG LEU ALA ALA GLU ARG SEQRES 5 A 305 GLY ILE PRO VAL TYR ALA PRO ASP ASN VAL ASN HIS PRO SEQRES 6 A 305 LEU TRP VAL GLU ARG ILE ALA GLN LEU SER PRO ASP VAL SEQRES 7 A 305 ILE PHE SER PHE TYR TYR ARG HIS LEU ILE TYR ASP GLU SEQRES 8 A 305 ILE LEU GLN LEU ALA PRO ALA GLY ALA PHE ASN LEU HIS SEQRES 9 A 305 GLY SER LEU LEU PRO LYS TYR ARG GLY ARG ALA PRO LEU SEQRES 10 A 305 ASN TRP VAL LEU VAL ASN GLY GLU THR GLU THR GLY VAL SEQRES 11 A 305 THR LEU HIS ARG MET VAL LYS ARG ALA ASP ALA GLY ALA SEQRES 12 A 305 ILE VAL ALA GLN LEU ARG ILE ALA ILE ALA PRO ASP ASP SEQRES 13 A 305 ILE ALA ILE THR LEU HIS HIS LYS LEU CYS HIS ALA ALA SEQRES 14 A 305 ARG GLN LEU LEU GLU GLN THR LEU PRO ALA ILE LYS HIS SEQRES 15 A 305 GLY ASN ILE LEU GLU ILE ALA GLN ARG GLU ASN GLU ALA SEQRES 16 A 305 THR CYS PHE GLY ARG ARG THR PRO ASP ASP SER PHE LEU SEQRES 17 A 305 GLU TRP HIS LYS PRO ALA SER VAL LEU HIS ASN MET VAL SEQRES 18 A 305 ARG ALA VAL ALA ASP PRO TRP PRO GLY ALA PHE SER TYR SEQRES 19 A 305 VAL GLY ASN GLN LYS PHE THR VAL TRP SER SER ARG VAL SEQRES 20 A 305 HIS PRO HIS ALA SER LYS ALA GLN PRO GLY SER VAL ILE SEQRES 21 A 305 SER VAL ALA PRO LEU LEU ILE ALA CYS GLY ASP GLY ALA SEQRES 22 A 305 LEU GLU ILE VAL THR GLY GLN ALA GLY ASP GLY ILE THR SEQRES 23 A 305 MET GLN GLY SER GLN LEU ALA GLN THR LEU GLY LEU VAL SEQRES 24 A 305 GLN GLY SER ARG LEU ASN SEQRES 1 B 305 MET LYS THR VAL VAL PHE ALA TYR HIS ASP MET GLY CYS SEQRES 2 B 305 LEU GLY ILE GLU ALA LEU LEU ALA ALA GLY TYR GLU ILE SEQRES 3 B 305 SER ALA ILE PHE THR HIS THR ASP ASN PRO GLY GLU LYS SEQRES 4 B 305 ALA PHE TYR GLY SER VAL ALA ARG LEU ALA ALA GLU ARG SEQRES 5 B 305 GLY ILE PRO VAL TYR ALA PRO ASP ASN VAL ASN HIS PRO SEQRES 6 B 305 LEU TRP VAL GLU ARG ILE ALA GLN LEU SER PRO ASP VAL SEQRES 7 B 305 ILE PHE SER PHE TYR TYR ARG HIS LEU ILE TYR ASP GLU SEQRES 8 B 305 ILE LEU GLN LEU ALA PRO ALA GLY ALA PHE ASN LEU HIS SEQRES 9 B 305 GLY SER LEU LEU PRO LYS TYR ARG GLY ARG ALA PRO LEU SEQRES 10 B 305 ASN TRP VAL LEU VAL ASN GLY GLU THR GLU THR GLY VAL SEQRES 11 B 305 THR LEU HIS ARG MET VAL LYS ARG ALA ASP ALA GLY ALA SEQRES 12 B 305 ILE VAL ALA GLN LEU ARG ILE ALA ILE ALA PRO ASP ASP SEQRES 13 B 305 ILE ALA ILE THR LEU HIS HIS LYS LEU CYS HIS ALA ALA SEQRES 14 B 305 ARG GLN LEU LEU GLU GLN THR LEU PRO ALA ILE LYS HIS SEQRES 15 B 305 GLY ASN ILE LEU GLU ILE ALA GLN ARG GLU ASN GLU ALA SEQRES 16 B 305 THR CYS PHE GLY ARG ARG THR PRO ASP ASP SER PHE LEU SEQRES 17 B 305 GLU TRP HIS LYS PRO ALA SER VAL LEU HIS ASN MET VAL SEQRES 18 B 305 ARG ALA VAL ALA ASP PRO TRP PRO GLY ALA PHE SER TYR SEQRES 19 B 305 VAL GLY ASN GLN LYS PHE THR VAL TRP SER SER ARG VAL SEQRES 20 B 305 HIS PRO HIS ALA SER LYS ALA GLN PRO GLY SER VAL ILE SEQRES 21 B 305 SER VAL ALA PRO LEU LEU ILE ALA CYS GLY ASP GLY ALA SEQRES 22 B 305 LEU GLU ILE VAL THR GLY GLN ALA GLY ASP GLY ILE THR SEQRES 23 B 305 MET GLN GLY SER GLN LEU ALA GLN THR LEU GLY LEU VAL SEQRES 24 B 305 GLN GLY SER ARG LEU ASN HET FON A1305 34 HET U5P A1306 21 HET ACT A1307 4 HET FON B1305 34 HET U5P B1306 21 HET ACT B1307 4 HETNAM FON N-{[4-({[(6R)-2-AMINO-5-FORMYL-4-OXO-1,4,5,6,7,8- HETNAM 2 FON HEXAHYDROPTERIDIN-6-YL]METHYL}AMINO)PHENYL]CARBONYL}- HETNAM 3 FON L-GLUTAMIC ACID HETNAM U5P URIDINE-5'-MONOPHOSPHATE HETNAM ACT ACETATE ION HETSYN FON [6R]-5-FORMYL-5,6,7,8-TETRAHYDROFOLATE; 6R-FOLINIC ACID FORMUL 3 FON 2(C20 H23 N7 O7) FORMUL 4 U5P 2(C9 H13 N2 O9 P) FORMUL 5 ACT 2(C2 H3 O2 1-) FORMUL 9 HOH *648(H2 O) HELIX 1 1 TYR A 8 ALA A 22 1 15 HELIX 2 2 SER A 44 GLY A 53 1 10 HELIX 3 3 HIS A 64 LEU A 74 1 11 HELIX 4 4 TYR A 89 GLN A 94 1 6 HELIX 5 5 ALA A 115 ASN A 123 1 9 HELIX 6 6 ILE A 157 HIS A 182 1 26 HELIX 7 7 ARG A 191 ALA A 195 5 5 HELIX 8 8 THR A 202 SER A 206 5 5 HELIX 9 9 PRO A 213 VAL A 224 1 12 HELIX 10 10 GLY A 289 GLY A 297 1 9 HELIX 11 11 TYR B 8 ALA B 22 1 15 HELIX 12 12 SER B 44 GLY B 53 1 10 HELIX 13 13 HIS B 64 GLN B 73 1 10 HELIX 14 14 TYR B 89 GLN B 94 1 6 HELIX 15 15 ALA B 115 ASN B 123 1 9 HELIX 16 16 ILE B 157 HIS B 182 1 26 HELIX 17 17 ARG B 191 ALA B 195 5 5 HELIX 18 18 THR B 202 SER B 206 5 5 HELIX 19 19 PRO B 213 VAL B 224 1 12 HELIX 20 20 GLY B 289 LEU B 296 1 8 SHEET 1 AA 7 VAL A 56 TYR A 57 0 SHEET 2 AA 7 GLU A 25 PHE A 30 1 O ILE A 29 N TYR A 57 SHEET 3 AA 7 LYS A 2 ALA A 7 1 O THR A 3 N SER A 27 SHEET 4 AA 7 VAL A 78 PHE A 82 1 O VAL A 78 N VAL A 4 SHEET 5 AA 7 ALA A 100 HIS A 104 1 O PHE A 101 N SER A 81 SHEET 6 AA 7 GLU A 127 ARG A 134 -1 O THR A 131 N HIS A 104 SHEET 7 AA 7 ILE A 144 ALA A 151 -1 N VAL A 145 O LEU A 132 SHEET 1 AB 2 ARG A 112 GLY A 113 0 SHEET 2 AB 2 CYS A 197 PHE A 198 1 N PHE A 198 O ARG A 112 SHEET 1 AC 5 ALA A 231 VAL A 235 0 SHEET 2 AC 5 GLN A 238 HIS A 248 -1 O GLN A 238 N VAL A 235 SHEET 3 AC 5 ALA A 273 ALA A 281 -1 O ALA A 273 N HIS A 248 SHEET 4 AC 5 LEU A 265 ALA A 268 -1 O LEU A 265 N ILE A 276 SHEET 5 AC 5 VAL A 259 SER A 261 -1 N ILE A 260 O LEU A 266 SHEET 1 AD 4 ALA A 231 VAL A 235 0 SHEET 2 AD 4 GLN A 238 HIS A 248 -1 O GLN A 238 N VAL A 235 SHEET 3 AD 4 ALA A 273 ALA A 281 -1 O ALA A 273 N HIS A 248 SHEET 4 AD 4 MET A 287 GLN A 288 -1 O MET A 287 N GLY A 279 SHEET 1 BA 7 VAL B 56 TYR B 57 0 SHEET 2 BA 7 GLU B 25 PHE B 30 1 O ILE B 29 N TYR B 57 SHEET 3 BA 7 LYS B 2 ALA B 7 1 O THR B 3 N SER B 27 SHEET 4 BA 7 VAL B 78 PHE B 82 1 O VAL B 78 N VAL B 4 SHEET 5 BA 7 ALA B 100 HIS B 104 1 O PHE B 101 N SER B 81 SHEET 6 BA 7 GLU B 127 ARG B 134 -1 O THR B 131 N HIS B 104 SHEET 7 BA 7 ILE B 144 ALA B 151 -1 N VAL B 145 O LEU B 132 SHEET 1 BB 2 ARG B 112 GLY B 113 0 SHEET 2 BB 2 CYS B 197 PHE B 198 1 N PHE B 198 O ARG B 112 SHEET 1 BC 5 ALA B 231 VAL B 235 0 SHEET 2 BC 5 GLN B 238 HIS B 248 -1 O GLN B 238 N VAL B 235 SHEET 3 BC 5 ALA B 273 ALA B 281 -1 O ALA B 273 N HIS B 248 SHEET 4 BC 5 LEU B 265 ALA B 268 -1 O LEU B 265 N ILE B 276 SHEET 5 BC 5 VAL B 259 SER B 261 -1 N ILE B 260 O LEU B 266 SHEET 1 BD 4 ALA B 231 VAL B 235 0 SHEET 2 BD 4 GLN B 238 HIS B 248 -1 O GLN B 238 N VAL B 235 SHEET 3 BD 4 ALA B 273 ALA B 281 -1 O ALA B 273 N HIS B 248 SHEET 4 BD 4 MET B 287 GLN B 288 -1 O MET B 287 N GLY B 279 CISPEP 1 LEU A 108 PRO A 109 0 10.36 CISPEP 2 ASP A 226 PRO A 227 0 10.59 CISPEP 3 ALA A 263 PRO A 264 0 3.68 CISPEP 4 LEU B 108 PRO B 109 0 10.60 CISPEP 5 ASP B 226 PRO B 227 0 11.58 CISPEP 6 ALA B 263 PRO B 264 0 4.85 SITE 1 AC1 6 MET A 11 TYR A 83 LEU A 117 HIS A 162 SITE 2 AC1 6 HOH A2126 HOH A2293 SITE 1 AC2 6 MET B 11 TYR B 83 LEU B 117 HIS B 162 SITE 2 AC2 6 HOH B2354 HOH B2355 SITE 1 AC3 19 TYR A 84 HIS A 86 LEU A 87 ILE A 88 SITE 2 AC3 19 LEU A 93 ASN A 102 ARG A 114 MET A 135 SITE 3 AC3 19 VAL A 136 ALA A 139 ASP A 140 HOH A2097 SITE 4 AC3 19 HOH A2149 HOH A2284 HOH A2285 HOH A2286 SITE 5 AC3 19 HOH A2287 HOH A2288 GLU B 194 SITE 1 AC4 14 TYR A 42 ARG A 85 ASN A 118 ARG A 200 SITE 2 AC4 14 ARG A 201 THR A 202 PRO A 203 VAL A 224 SITE 3 AC4 14 PRO A 229 HOH A2198 HOH A2289 HOH A2290 SITE 4 AC4 14 HOH A2291 HOH A2292 SITE 1 AC5 21 HIS A 211 SER B 81 TYR B 84 HIS B 86 SITE 2 AC5 21 LEU B 87 ILE B 88 LEU B 93 ASN B 102 SITE 3 AC5 21 ARG B 114 MET B 135 VAL B 136 ALA B 139 SITE 4 AC5 21 ASP B 140 HOH B2117 HOH B2178 HOH B2342 SITE 5 AC5 21 HOH B2343 HOH B2344 HOH B2345 HOH B2346 SITE 6 AC5 21 HOH B2347 SITE 1 AC6 15 HIS B 9 TYR B 42 ARG B 85 ASN B 118 SITE 2 AC6 15 ARG B 201 THR B 202 PRO B 203 VAL B 224 SITE 3 AC6 15 PRO B 229 HOH B2243 HOH B2248 HOH B2349 SITE 4 AC6 15 HOH B2350 HOH B2351 HOH B2353 CRYST1 67.176 89.957 97.885 90.00 90.00 90.00 P 21 21 21 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 0.014886 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011116 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010216 0.00000