HEADER CARBOHYDRATE KINASE 29-NOV-97 1RKD TITLE E. COLI RIBOKINASE COMPLEXED WITH RIBOSE AND ADP COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBOKINASE; COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.1.15; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 CELL_LINE: S2; SOURCE 6 CELLULAR_LOCATION: CYTOPLASM; SOURCE 7 GENE: RBSK; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: MRI240; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PJGK10; SOURCE 12 OTHER_DETAILS: THE RBSK GENE WAS CLONED BEHIND A TRP-PROMOTER, SOURCE 13 FORMING THE PLASMID PJGK10 KEYWDS CARBOHYDRATE KINASE, RIBOSE, NUCLEOTIDE BINDING, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.A.SIGRELL,A.D.CAMERON,T.A.JONES,S.L.MOWBRAY REVDAT 6 14-FEB-24 1RKD 1 HETSYN REVDAT 5 29-JUL-20 1RKD 1 COMPND REMARK HETNAM SITE REVDAT 5 2 1 ATOM REVDAT 4 13-JUL-11 1RKD 1 VERSN REVDAT 3 24-FEB-09 1RKD 1 VERSN REVDAT 2 01-APR-03 1RKD 1 JRNL REVDAT 1 04-MAR-98 1RKD 0 JRNL AUTH J.A.SIGRELL,A.D.CAMERON,T.A.JONES,S.L.MOWBRAY JRNL TITL STRUCTURE OF ESCHERICHIA COLI RIBOKINASE IN COMPLEX WITH JRNL TITL 2 RIBOSE AND DINUCLEOTIDE DETERMINED TO 1.8 A RESOLUTION: JRNL TITL 3 INSIGHTS INTO A NEW FAMILY OF KINASE STRUCTURES. JRNL REF STRUCTURE V. 6 183 1998 JRNL REFN ISSN 0969-2126 JRNL PMID 9519409 JRNL DOI 10.1016/S0969-2126(98)00020-3 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.A.SIGRELL,A.D.CAMERON,T.A.JONES,S.L.MOWBRAY REMARK 1 TITL PURIFICATION, CHARACTERIZATION, AND CRYSTALLIZATION OF REMARK 1 TITL 2 ESCHERICHIA COLI RIBOKINASE REMARK 1 REF PROTEIN SCI. V. 6 2474 1997 REMARK 1 REFN ISSN 0961-8368 REMARK 1 REFERENCE 2 REMARK 1 AUTH J.N.HOPE,A.W.BELL,M.A.HERMODSON,J.M.GROARKE REMARK 1 TITL RIBOKINASE FROM ESCHERICHIA COLI K12. NUCLEOTIDE SEQUENCE REMARK 1 TITL 2 AND OVEREXPRESSION OF THE RBSK GENE AND PURIFICATION OF REMARK 1 TITL 3 RIBOKINASE REMARK 1 REF J.BIOL.CHEM. V. 261 7663 1986 REMARK 1 REFN ISSN 0021-9258 REMARK 2 REMARK 2 RESOLUTION. 1.84 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.84 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 35013 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) : 0.221 REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3542 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2248 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 47 REMARK 3 SOLVENT ATOMS : 181 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.013 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.028 ; 0.040 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.033 ; 0.050 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.020 ; 0.030 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.130 ; 0.150 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.180 ; 0.300 REMARK 3 MULTIPLE TORSION (A) : 0.250 ; 0.300 REMARK 3 H-BOND (X...Y) (A) : 0.150 ; 0.300 REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : 4.200 ; 7.000 REMARK 3 STAGGERED (DEGREES) : 16.200; 15.000 REMARK 3 TRANSVERSE (DEGREES) : 29.600; 20.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.400 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.000 ; 2.500 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.500 ; 4.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.000 ; 6.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE BULK SOLVENT CORRECTION WAS REMARK 3 CALCULATED IN X-PLOR. AMP-PNP WAS INCLUDED IN THE REMARK 3 CRYSTALLIZATION MIXTURE, BUT THE GAMMA-PHOSPHATE COULD NOT BE REMARK 3 DETECTED. THE AUTHORS THEREFORE TREAT HYDROLYSED ATP-ANALOGUE AS REMARK 3 ADP IN THE MODEL. REMARK 4 REMARK 4 1RKD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000176102. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NOV-96 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : 8.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : BW7B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8893 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE 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 : 35015 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.840 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 30.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.84 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.87 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.8 REMARK 200 DATA REDUNDANCY IN SHELL : 7.50 REMARK 200 R MERGE FOR SHELL (I) : 0.23900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MULTIPLE ISOMORPHOUS REMARK 200 REPLACEMENT REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS WERE GROWN IN THE PRESENCE OF REMARK 280 0.5 MM RIBOSE, 10 MM AMP-PNP AND 10 MM MGCL2 USING 2.1-2.4 M REMARK 280 NH4H2PO4 AS PRECIPITANT AND BUFFERED TO PH 8.4 WITH 0.1 M TRIS- REMARK 280 HCL. REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 51.62333 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 103.24667 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 77.43500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 129.05833 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 25.81167 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 51.62333 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 103.24667 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 129.05833 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 77.43500 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 25.81167 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 5260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -47.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 103.24667 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 P PO4 A 313 LIES ON A SPECIAL POSITION. 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 GLN A 2 REMARK 465 ASN A 3 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 OD2 ASP A 66 OD2 ASP A 66 11555 2.19 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 GLU A 29 OE1 - CD - OE2 ANGL. DEV. = 8.6 DEGREES REMARK 500 ARG A 53 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ASP A 66 CB - CG - OD2 ANGL. DEV. = -8.5 DEGREES REMARK 500 ARG A 227 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG A 227 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 276 CD - NE - CZ 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 34 -103.23 -113.00 REMARK 500 GLN A 141 -166.95 -129.85 REMARK 500 ASN A 234 53.95 39.32 REMARK 500 ALA A 291 -85.13 -96.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 GLU A 176 11.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: RB1 REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: RESIDUES MAKING DIRECT HYDROGEN BONDS WITH REMARK 800 RIBOSE. REMARK 800 REMARK 800 SITE_IDENTIFIER: RB2 REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: RESIDUES MAKING WATER-MEDIATED HYDROGEN BONDS REMARK 800 WITH RIBOSE. REMARK 800 REMARK 800 SITE_IDENTIFIER: RB3 REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: RESIDUES WITHIN VAN DER WAALS DISTANCE OF REMARK 800 RIBOSE. REMARK 800 REMARK 800 SITE_IDENTIFIER: AB1 REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: RESIDUES MAKING DIRECT HYDROGEN BONDS WITH ADP. REMARK 800 REMARK 800 SITE_IDENTIFIER: AB2 REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: RESIDUES MAKING WATER-MEDIATED HYDROGEN BONDS REMARK 800 WITH ADP. REMARK 800 REMARK 800 SITE_IDENTIFIER: AB3 REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: RESIDUES WITHIN VAN DER WAALS DISTANCE OF ADP. DBREF 1RKD A 1 309 UNP P0A9J6 RBSK_ECOLI 1 309 SEQRES 1 A 309 MET GLN ASN ALA GLY SER LEU VAL VAL LEU GLY SER ILE SEQRES 2 A 309 ASN ALA ASP HIS ILE LEU ASN LEU GLN SER PHE PRO THR SEQRES 3 A 309 PRO GLY GLU THR VAL THR GLY ASN HIS TYR GLN VAL ALA SEQRES 4 A 309 PHE GLY GLY LYS GLY ALA ASN GLN ALA VAL ALA ALA GLY SEQRES 5 A 309 ARG SER GLY ALA ASN ILE ALA PHE ILE ALA CYS THR GLY SEQRES 6 A 309 ASP ASP SER ILE GLY GLU SER VAL ARG GLN GLN LEU ALA SEQRES 7 A 309 THR ASP ASN ILE ASP ILE THR PRO VAL SER VAL ILE LYS SEQRES 8 A 309 GLY GLU SER THR GLY VAL ALA LEU ILE PHE VAL ASN GLY SEQRES 9 A 309 GLU GLY GLU ASN VAL ILE GLY ILE HIS ALA GLY ALA ASN SEQRES 10 A 309 ALA ALA LEU SER PRO ALA LEU VAL GLU ALA GLN ARG GLU SEQRES 11 A 309 ARG ILE ALA ASN ALA SER ALA LEU LEU MET GLN LEU GLU SEQRES 12 A 309 SER PRO LEU GLU SER VAL MET ALA ALA ALA LYS ILE ALA SEQRES 13 A 309 HIS GLN ASN LYS THR ILE VAL ALA LEU ASN PRO ALA PRO SEQRES 14 A 309 ALA ARG GLU LEU PRO ASP GLU LEU LEU ALA LEU VAL ASP SEQRES 15 A 309 ILE ILE THR PRO ASN GLU THR GLU ALA GLU LYS LEU THR SEQRES 16 A 309 GLY ILE ARG VAL GLU ASN ASP GLU ASP ALA ALA LYS ALA SEQRES 17 A 309 ALA GLN VAL LEU HIS GLU LYS GLY ILE ARG THR VAL LEU SEQRES 18 A 309 ILE THR LEU GLY SER ARG GLY VAL TRP ALA SER VAL ASN SEQRES 19 A 309 GLY GLU GLY GLN ARG VAL PRO GLY PHE ARG VAL GLN ALA SEQRES 20 A 309 VAL ASP THR ILE ALA ALA GLY ASP THR PHE ASN GLY ALA SEQRES 21 A 309 LEU ILE THR ALA LEU LEU GLU GLU LYS PRO LEU PRO GLU SEQRES 22 A 309 ALA ILE ARG PHE ALA HIS ALA ALA ALA ALA ILE ALA VAL SEQRES 23 A 309 THR ARG LYS GLY ALA GLN PRO SER VAL PRO TRP ARG GLU SEQRES 24 A 309 GLU ILE ASP ALA PHE LEU ASP ARG GLN ARG HET RIB A 311 10 HET PO4 A 312 5 HET PO4 A 313 5 HET ADP A 310 27 HETNAM RIB ALPHA-D-RIBOFURANOSE HETNAM PO4 PHOSPHATE ION HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETSYN RIB ALPHA-D-RIBOSE; D-RIBOSE; RIBOSE FORMUL 2 RIB C5 H10 O5 FORMUL 3 PO4 2(O4 P 3-) FORMUL 5 ADP C10 H15 N5 O10 P2 FORMUL 6 HOH *181(H2 O) HELIX 1 H1 LYS A 43 SER A 54 1 12 HELIX 2 H2 SER A 68 THR A 79 1 12 HELIX 3 H3 PRO A 122 ASN A 134 1 13 HELIX 4 H4 LEU A 146 ASN A 159 1 14 HELIX 5 H5 ASP A 175 LEU A 180 1 6 HELIX 6 H6 GLU A 188 LEU A 194 1 7 HELIX 7 H7 GLU A 203 LYS A 215 1 13 HELIX 8 H8 ALA A 253 GLU A 267 1 15 HELIX 9 H9 LEU A 271 THR A 287 1 17 HELIX 10 H10 ARG A 298 ARG A 307 1 10 SHEET 1 S1 9 VAL A 87 LYS A 91 0 SHEET 2 S1 9 ILE A 58 GLY A 65 1 SHEET 3 S1 9 SER A 6 LEU A 10 1 SHEET 4 S1 9 ALA A 137 GLN A 141 1 SHEET 5 S1 9 ILE A 162 ASN A 166 1 SHEET 6 S1 9 ILE A 183 ASN A 187 1 SHEET 7 S1 9 THR A 219 LEU A 224 1 SHEET 8 S1 9 TRP A 230 VAL A 233 -1 SHEET 9 S1 9 GLU A 236 GLY A 242 -1 SHEET 1 S2 4 GLU A 29 VAL A 38 0 SHEET 2 S2 4 SER A 12 LEU A 21 -1 SHEET 3 S2 4 GLY A 96 ASN A 103 1 SHEET 4 S2 4 GLU A 107 ALA A 114 -1 CISPEP 1 ALA A 168 PRO A 169 0 -5.21 SITE 1 RB1 7 ASN A 14 ASP A 16 GLY A 42 LYS A 43 SITE 2 RB1 7 ASN A 46 GLU A 143 ASP A 255 SITE 1 RB2 3 ALA A 252 GLY A 254 ASP A 255 SITE 1 RB3 5 ALA A 98 ILE A 100 ILE A 110 ILE A 112 SITE 2 RB3 5 ILE A 251 SITE 1 AB1 4 ASN A 187 THR A 223 GLY A 225 ALA A 280 SITE 1 AB2 7 ASN A 166 ASN A 187 GLU A 190 THR A 223 SITE 2 AB2 7 PHE A 243 VAL A 245 ALA A 280 SITE 1 AB3 5 GLY A 225 VAL A 245 ALA A 253 ALA A 282 SITE 2 AB3 5 VAL A 286 CRYST1 95.400 95.400 154.870 90.00 90.00 120.00 P 61 2 2 12 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 0.010482 0.006052 0.000000 0.00000 SCALE2 0.000000 0.012104 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006457 0.00000