HEADER TRANSFERASE 28-APR-09 3H86 TITLE CRYSTAL STRUCTURE OF ADENYLATE KINASE FROM METHANOCOCCUS MARIPALUDIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADENYLATE KINASE; COMPND 3 CHAIN: B, A, C, G; COMPND 4 SYNONYM: AK, ATP-AMP TRANSPHOSPHORYLASE; COMPND 5 EC: 2.7.4.3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOCOCCUS MARIPALUDIS; SOURCE 3 ORGANISM_TAXID: 39152; SOURCE 4 STRAIN: ATCC 43000D; SOURCE 5 GENE: ADK, ADKA, MMP1031; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA 2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS MESOPHILE, KINASE, ADENYLATE KINASE, PHOSPHOTRANSFERASE, ATP-BINDING, KEYWDS 2 CYTOPLASM, NUCLEOTIDE-BINDING, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR D.G.MILYA,S.YOUSIF REVDAT 5 29-NOV-23 3H86 1 REMARK REVDAT 4 06-SEP-23 3H86 1 REMARK SEQADV REVDAT 3 01-NOV-17 3H86 1 REMARK REVDAT 2 22-DEC-09 3H86 1 JRNL REVDAT 1 06-OCT-09 3H86 0 JRNL AUTH M.DAVLIEVA,Y.SHAMOO JRNL TITL CRYSTAL STRUCTURE OF A TRIMERIC ARCHAEAL ADENYLATE KINASE JRNL TITL 2 FROM THE MESOPHILE METHANOCOCCUS MARIPALUDIS WITH AN JRNL TITL 3 UNUSUALLY BROAD FUNCTIONAL RANGE AND THERMAL STABILITY. JRNL REF PROTEINS V. 78 357 2009 JRNL REFN ISSN 0887-3585 JRNL PMID 19731371 JRNL DOI 10.1002/PROT.22549 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 5.5.0070 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.70 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 27970 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3138 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 2.5640 - 2.5000 1.00 2066 211 0.1850 0.2820 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 59.47 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 9.05000 REMARK 3 B22 (A**2) : 9.05000 REMARK 3 B33 (A**2) : -18.10000 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 TWINNING INFORMATION. REMARK 3 FRACTION: 0.6090 REMARK 3 OPERATOR: H, K, L REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : 0.124 976 REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3H86 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-JUN-09. REMARK 100 THE DEPOSITION ID IS D_1000052813. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-AUG-08 REMARK 200 TEMPERATURE (KELVIN) : 103 REMARK 200 PH : 4.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : RIGAKU OSMIC MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31158 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 29.690 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 2.440 REMARK 200 R MERGE (I) : 0.08200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.33000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER FOR MR REMARK 200 STARTING MODEL: PDB ENTRY 1KHT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.4 M AMMONIUM CHLORIDE, 0.1 M SODIUM REMARK 280 ACETATE, 3% ETHYLENE GLYCOL (V/V)., PH 4.7, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 273K 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 51.42000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 29.68735 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 76.24000 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 51.42000 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 29.68735 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 76.24000 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 51.42000 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 29.68735 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 76.24000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 59.37470 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 152.48000 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 59.37470 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 152.48000 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 59.37470 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 152.48000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, A, C 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -49.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: G 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 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DODECAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 44640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 86880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -256.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: G REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 51.42000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 29.68735 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 76.24000 REMARK 350 BIOMT1 2 -0.500000 -0.866025 0.000000 51.42000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 29.68735 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 76.24000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 51.42000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 29.68735 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 76.24000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, A, C REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 5 -0.500000 -0.866025 0.000000 102.84000 REMARK 350 BIOMT2 5 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 6 -0.500000 0.866025 0.000000 51.42000 REMARK 350 BIOMT2 6 -0.866025 -0.500000 0.000000 89.06205 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 0.00000 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 HOH G 195 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 B 1 REMARK 465 MET A 1 REMARK 465 MET C 1 REMARK 465 MET G 1 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 NH2 ARG B 140 O1G AP5 B 193 1.47 REMARK 500 OE1 GLN B 152 O HOH B 198 2.04 REMARK 500 O2G AP5 A 193 O HOH A 195 2.12 REMARK 500 ND2 ASN G 3 O ALA G 82 2.14 REMARK 500 O HOH A 201 O HOH A 204 2.15 REMARK 500 O3A AP5 A 193 O HOH A 195 2.18 REMARK 500 OD1 ASN G 48 O ALA G 53 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 SER C 28 OE2 GLU G 80 2555 2.10 REMARK 500 OD2 ASP A 63 NH1 ARG G 69 2555 2.16 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 GLU B 149 CG GLU B 149 CD 0.108 REMARK 500 GLU B 149 CD GLU B 149 OE2 0.078 REMARK 500 VAL C 180 CB VAL C 180 CG2 0.130 REMARK 500 TYR G 101 CE2 TYR G 101 CD2 -0.104 REMARK 500 GLU G 149 CG GLU G 149 CD 0.099 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 C 98 C - N - CA ANGL. DEV. = 9.8 DEGREES REMARK 500 ARG C 156 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG G 156 NE - CZ - NH2 ANGL. DEV. = -3.8 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 B 3 -141.35 64.89 REMARK 500 TYR B 34 -147.16 -84.46 REMARK 500 LYS B 35 102.02 -162.31 REMARK 500 ALA B 47 -75.72 -57.75 REMARK 500 SER B 54 -80.67 -91.18 REMARK 500 ASP B 55 160.57 -46.28 REMARK 500 MET B 59 -17.36 -142.00 REMARK 500 MET B 81 -2.91 -54.27 REMARK 500 THR B 91 -161.87 -160.15 REMARK 500 LYS B 96 77.91 -68.04 REMARK 500 LYS B 99 22.92 -76.99 REMARK 500 LEU B 105 78.01 -105.26 REMARK 500 GLU B 112 8.79 -66.11 REMARK 500 LEU B 113 -61.56 -141.26 REMARK 500 ASN B 114 74.90 56.52 REMARK 500 LEU B 142 75.30 74.39 REMARK 500 ALA B 158 -70.78 -47.92 REMARK 500 ALA B 159 -46.09 -29.31 REMARK 500 THR A 17 -70.86 -66.69 REMARK 500 ASP A 25 -59.78 -28.98 REMARK 500 GLU A 30 18.00 -149.71 REMARK 500 ASP A 45 -32.85 -35.51 REMARK 500 THR A 91 -150.44 -141.34 REMARK 500 PRO A 103 177.46 -56.49 REMARK 500 LEU A 105 79.14 -155.51 REMARK 500 PRO A 106 174.36 -59.98 REMARK 500 SER A 134 58.14 -94.94 REMARK 500 SER A 137 -5.40 -50.75 REMARK 500 LYS A 139 69.90 -151.17 REMARK 500 LEU A 142 82.61 50.46 REMARK 500 VAL C 37 153.71 -44.71 REMARK 500 ALA C 47 -61.06 -107.99 REMARK 500 ASP C 55 -174.14 -176.80 REMARK 500 GLN C 71 -62.38 -93.13 REMARK 500 LYS C 72 2.99 -60.05 REMARK 500 LYS C 83 35.00 -79.59 REMARK 500 GLU C 84 -45.18 -148.86 REMARK 500 THR C 91 -159.97 -138.82 REMARK 500 LEU C 105 70.64 -150.44 REMARK 500 ALA C 107 -57.60 -29.93 REMARK 500 ASN C 114 82.86 47.55 REMARK 500 THR C 123 176.20 173.50 REMARK 500 LEU C 142 55.42 28.33 REMARK 500 LEU C 179 38.96 -89.29 REMARK 500 GLU C 185 -34.98 83.70 REMARK 500 GLU G 30 -1.46 -55.58 REMARK 500 ASN G 33 66.12 -115.20 REMARK 500 ALA G 42 -78.09 -53.01 REMARK 500 MET G 43 -0.88 -59.03 REMARK 500 LEU G 62 153.23 -43.71 REMARK 500 REMARK 500 THIS ENTRY HAS 58 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AP5 B 193 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AP5 A 193 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AP5 C 193 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AP5 G 193 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1KHT RELATED DB: PDB REMARK 900 ADENYLATE KINASE FROM MESOPHILE METHANOCOCCUS VOLTAE REMARK 900 RELATED ID: 1KI9 RELATED DB: PDB REMARK 900 ADENYLATE KINASE FROM THERMOPHILE METHANOCOCCUS THERMOLITHOTROPHICUS DBREF 3H86 B 1 192 UNP Q6LYG0 KADA_METMP 1 192 DBREF 3H86 A 1 192 UNP Q6LYG0 KADA_METMP 1 192 DBREF 3H86 C 1 192 UNP Q6LYG0 KADA_METMP 1 192 DBREF 3H86 G 1 192 UNP Q6LYG0 KADA_METMP 1 192 SEQADV 3H86 LYS B 61 UNP Q6LYG0 ARG 61 VARIANT SEQADV 3H86 LYS A 61 UNP Q6LYG0 ARG 61 VARIANT SEQADV 3H86 LYS C 61 UNP Q6LYG0 ARG 61 VARIANT SEQADV 3H86 LYS G 61 UNP Q6LYG0 ARG 61 VARIANT SEQRES 1 B 192 MET LYS ASN LYS VAL VAL VAL VAL THR GLY VAL PRO GLY SEQRES 2 B 192 VAL GLY GLY THR THR VAL THR GLN LYS ALA MET ASP ILE SEQRES 3 B 192 LEU SER GLU GLU GLY LEU ASN TYR LYS MET VAL ASN PHE SEQRES 4 B 192 GLY SER ALA MET PHE ASP VAL ALA ASN GLU GLU GLY LEU SEQRES 5 B 192 ALA SER ASP ARG ASP GLN MET ARG LYS LEU ASP PRO GLU SEQRES 6 B 192 THR GLN LYS ARG ILE GLN LYS MET ALA GLY ARG LYS ILE SEQRES 7 B 192 ALA GLU MET ALA LYS GLU SER PRO VAL ALA VAL ASP THR SEQRES 8 B 192 HIS SER THR VAL LYS THR PRO LYS GLY TYR LEU PRO GLY SEQRES 9 B 192 LEU PRO ALA TRP VAL LEU THR GLU LEU ASN PRO ASP ILE SEQRES 10 B 192 VAL ILE VAL VAL GLU THR ASP GLY ASP GLU ILE LEU MET SEQRES 11 B 192 ARG ARG LEU SER ASP GLU SER ARG LYS ARG ASP LEU GLU SEQRES 12 B 192 THR THR ALA SER ILE GLU GLU HIS GLN PHE MET ASN ARG SEQRES 13 B 192 ALA ALA ALA MET SER TYR GLY VAL LEU THR GLY ALA THR SEQRES 14 B 192 VAL LYS ILE VAL LYS ASN LYS ASN GLY LEU VAL ASP ASN SEQRES 15 B 192 ALA VAL GLU GLU LEU MET SER VAL LEU ARG SEQRES 1 A 192 MET LYS ASN LYS VAL VAL VAL VAL THR GLY VAL PRO GLY SEQRES 2 A 192 VAL GLY GLY THR THR VAL THR GLN LYS ALA MET ASP ILE SEQRES 3 A 192 LEU SER GLU GLU GLY LEU ASN TYR LYS MET VAL ASN PHE SEQRES 4 A 192 GLY SER ALA MET PHE ASP VAL ALA ASN GLU GLU GLY LEU SEQRES 5 A 192 ALA SER ASP ARG ASP GLN MET ARG LYS LEU ASP PRO GLU SEQRES 6 A 192 THR GLN LYS ARG ILE GLN LYS MET ALA GLY ARG LYS ILE SEQRES 7 A 192 ALA GLU MET ALA LYS GLU SER PRO VAL ALA VAL ASP THR SEQRES 8 A 192 HIS SER THR VAL LYS THR PRO LYS GLY TYR LEU PRO GLY SEQRES 9 A 192 LEU PRO ALA TRP VAL LEU THR GLU LEU ASN PRO ASP ILE SEQRES 10 A 192 VAL ILE VAL VAL GLU THR ASP GLY ASP GLU ILE LEU MET SEQRES 11 A 192 ARG ARG LEU SER ASP GLU SER ARG LYS ARG ASP LEU GLU SEQRES 12 A 192 THR THR ALA SER ILE GLU GLU HIS GLN PHE MET ASN ARG SEQRES 13 A 192 ALA ALA ALA MET SER TYR GLY VAL LEU THR GLY ALA THR SEQRES 14 A 192 VAL LYS ILE VAL LYS ASN LYS ASN GLY LEU VAL ASP ASN SEQRES 15 A 192 ALA VAL GLU GLU LEU MET SER VAL LEU ARG SEQRES 1 C 192 MET LYS ASN LYS VAL VAL VAL VAL THR GLY VAL PRO GLY SEQRES 2 C 192 VAL GLY GLY THR THR VAL THR GLN LYS ALA MET ASP ILE SEQRES 3 C 192 LEU SER GLU GLU GLY LEU ASN TYR LYS MET VAL ASN PHE SEQRES 4 C 192 GLY SER ALA MET PHE ASP VAL ALA ASN GLU GLU GLY LEU SEQRES 5 C 192 ALA SER ASP ARG ASP GLN MET ARG LYS LEU ASP PRO GLU SEQRES 6 C 192 THR GLN LYS ARG ILE GLN LYS MET ALA GLY ARG LYS ILE SEQRES 7 C 192 ALA GLU MET ALA LYS GLU SER PRO VAL ALA VAL ASP THR SEQRES 8 C 192 HIS SER THR VAL LYS THR PRO LYS GLY TYR LEU PRO GLY SEQRES 9 C 192 LEU PRO ALA TRP VAL LEU THR GLU LEU ASN PRO ASP ILE SEQRES 10 C 192 VAL ILE VAL VAL GLU THR ASP GLY ASP GLU ILE LEU MET SEQRES 11 C 192 ARG ARG LEU SER ASP GLU SER ARG LYS ARG ASP LEU GLU SEQRES 12 C 192 THR THR ALA SER ILE GLU GLU HIS GLN PHE MET ASN ARG SEQRES 13 C 192 ALA ALA ALA MET SER TYR GLY VAL LEU THR GLY ALA THR SEQRES 14 C 192 VAL LYS ILE VAL LYS ASN LYS ASN GLY LEU VAL ASP ASN SEQRES 15 C 192 ALA VAL GLU GLU LEU MET SER VAL LEU ARG SEQRES 1 G 192 MET LYS ASN LYS VAL VAL VAL VAL THR GLY VAL PRO GLY SEQRES 2 G 192 VAL GLY GLY THR THR VAL THR GLN LYS ALA MET ASP ILE SEQRES 3 G 192 LEU SER GLU GLU GLY LEU ASN TYR LYS MET VAL ASN PHE SEQRES 4 G 192 GLY SER ALA MET PHE ASP VAL ALA ASN GLU GLU GLY LEU SEQRES 5 G 192 ALA SER ASP ARG ASP GLN MET ARG LYS LEU ASP PRO GLU SEQRES 6 G 192 THR GLN LYS ARG ILE GLN LYS MET ALA GLY ARG LYS ILE SEQRES 7 G 192 ALA GLU MET ALA LYS GLU SER PRO VAL ALA VAL ASP THR SEQRES 8 G 192 HIS SER THR VAL LYS THR PRO LYS GLY TYR LEU PRO GLY SEQRES 9 G 192 LEU PRO ALA TRP VAL LEU THR GLU LEU ASN PRO ASP ILE SEQRES 10 G 192 VAL ILE VAL VAL GLU THR ASP GLY ASP GLU ILE LEU MET SEQRES 11 G 192 ARG ARG LEU SER ASP GLU SER ARG LYS ARG ASP LEU GLU SEQRES 12 G 192 THR THR ALA SER ILE GLU GLU HIS GLN PHE MET ASN ARG SEQRES 13 G 192 ALA ALA ALA MET SER TYR GLY VAL LEU THR GLY ALA THR SEQRES 14 G 192 VAL LYS ILE VAL LYS ASN LYS ASN GLY LEU VAL ASP ASN SEQRES 15 G 192 ALA VAL GLU GLU LEU MET SER VAL LEU ARG HET AP5 B 193 57 HET AP5 A 193 57 HET AP5 C 193 57 HET AP5 G 193 57 HETNAM AP5 BIS(ADENOSINE)-5'-PENTAPHOSPHATE FORMUL 5 AP5 4(C20 H29 N10 O22 P5) FORMUL 9 HOH *43(H2 O) HELIX 1 1 GLY B 15 GLU B 29 1 15 HELIX 2 2 PHE B 39 MET B 43 1 5 HELIX 3 3 MET B 43 GLU B 49 1 7 HELIX 4 4 THR B 66 GLU B 84 1 19 HELIX 5 5 PRO B 106 GLU B 112 1 7 HELIX 6 6 ASP B 124 ASP B 135 1 12 HELIX 7 7 THR B 144 GLY B 167 1 24 HELIX 8 8 LEU B 179 ARG B 192 1 14 HELIX 9 9 GLY A 15 GLU A 29 1 15 HELIX 10 10 PHE A 39 ASN A 48 1 10 HELIX 11 11 ARG A 56 ARG A 60 5 5 HELIX 12 12 ASP A 63 GLU A 80 1 18 HELIX 13 13 PRO A 106 ASN A 114 1 9 HELIX 14 14 ASP A 124 ARG A 132 1 9 HELIX 15 15 THR A 144 GLY A 167 1 24 HELIX 16 16 LEU A 179 ARG A 192 1 14 HELIX 17 17 GLY C 15 GLU C 29 1 15 HELIX 18 18 ASN C 38 MET C 43 1 6 HELIX 19 19 ALA C 47 GLY C 51 5 5 HELIX 20 20 ASP C 63 LYS C 68 1 6 HELIX 21 21 MET C 73 ALA C 82 1 10 HELIX 22 22 PRO C 106 ASN C 114 1 9 HELIX 23 23 ASP C 124 ASP C 135 1 12 HELIX 24 24 THR C 144 GLY C 167 1 24 HELIX 25 25 LEU C 179 VAL C 184 1 6 HELIX 26 26 GLU C 185 ARG C 192 1 8 HELIX 27 27 GLY G 15 GLY G 31 1 17 HELIX 28 28 PHE G 39 GLU G 50 1 12 HELIX 29 29 ASP G 55 LYS G 61 5 7 HELIX 30 30 ASP G 63 SER G 85 1 23 HELIX 31 31 PRO G 106 ASN G 114 1 9 HELIX 32 32 ASP G 124 MET G 130 1 7 HELIX 33 33 MET G 130 ASP G 135 1 6 HELIX 34 34 THR G 144 GLY G 167 1 24 HELIX 35 35 LEU G 179 SER G 189 1 11 SHEET 1 A 5 MET B 36 ASN B 38 0 SHEET 2 A 5 VAL B 87 ASP B 90 1 O ASP B 90 N VAL B 37 SHEET 3 A 5 VAL B 5 THR B 9 1 N VAL B 8 O VAL B 89 SHEET 4 A 5 ILE B 117 GLU B 122 1 O ILE B 119 N THR B 9 SHEET 5 A 5 THR B 169 LYS B 174 1 O LYS B 171 N VAL B 120 SHEET 1 B 2 THR B 94 THR B 97 0 SHEET 2 B 2 GLY B 100 PRO B 103 -1 O LEU B 102 N VAL B 95 SHEET 1 C 5 LYS A 35 ASN A 38 0 SHEET 2 C 5 VAL A 87 THR A 91 1 O ASP A 90 N VAL A 37 SHEET 3 C 5 VAL A 5 THR A 9 1 N VAL A 6 O VAL A 89 SHEET 4 C 5 ILE A 117 GLU A 122 1 O ILE A 117 N VAL A 7 SHEET 5 C 5 THR A 169 LYS A 174 1 O THR A 169 N VAL A 118 SHEET 1 D 2 THR A 94 THR A 97 0 SHEET 2 D 2 GLY A 100 PRO A 103 -1 O LEU A 102 N VAL A 95 SHEET 1 E 4 VAL C 87 ASP C 90 0 SHEET 2 E 4 VAL C 5 THR C 9 1 N VAL C 6 O VAL C 89 SHEET 3 E 4 ILE C 117 GLU C 122 1 O ILE C 119 N THR C 9 SHEET 4 E 4 THR C 169 LYS C 174 1 O LYS C 171 N VAL C 120 SHEET 1 F 2 THR C 94 THR C 97 0 SHEET 2 F 2 GLY C 100 PRO C 103 -1 O GLY C 100 N THR C 97 SHEET 1 G 5 LYS G 35 ASN G 38 0 SHEET 2 G 5 VAL G 87 ASP G 90 1 O ASP G 90 N VAL G 37 SHEET 3 G 5 VAL G 5 THR G 9 1 N VAL G 6 O VAL G 87 SHEET 4 G 5 ILE G 117 GLU G 122 1 O ILE G 117 N VAL G 7 SHEET 5 G 5 THR G 169 LYS G 174 1 O LYS G 171 N VAL G 120 SHEET 1 H 2 THR G 94 THR G 97 0 SHEET 2 H 2 GLY G 100 PRO G 103 -1 O GLY G 100 N THR G 97 SITE 1 AC1 23 PRO B 12 GLY B 13 GLY B 15 GLY B 16 SITE 2 AC1 23 THR B 17 THR B 18 PHE B 39 GLY B 40 SITE 3 AC1 23 MET B 43 ARG B 56 GLN B 71 THR B 91 SITE 4 AC1 23 HIS B 92 VAL B 95 GLY B 104 ARG B 131 SITE 5 AC1 23 ASP B 135 ARG B 138 ARG B 140 ASN B 175 SITE 6 AC1 23 LYS B 176 ASN B 177 GLY B 178 SITE 1 AC2 27 PRO A 12 GLY A 13 VAL A 14 GLY A 15 SITE 2 AC2 27 GLY A 16 THR A 17 THR A 18 ASN A 38 SITE 3 AC2 27 GLY A 40 MET A 43 ARG A 56 ARG A 60 SITE 4 AC2 27 GLN A 71 THR A 91 HIS A 92 VAL A 95 SITE 5 AC2 27 GLY A 104 ARG A 131 SER A 134 ASP A 135 SITE 6 AC2 27 ARG A 138 ARG A 140 ASN A 175 LYS A 176 SITE 7 AC2 27 GLY A 178 VAL A 180 HOH A 195 SITE 1 AC3 21 PRO C 12 GLY C 13 VAL C 14 GLY C 15 SITE 2 AC3 21 THR C 17 THR C 18 PHE C 39 GLY C 40 SITE 3 AC3 21 ARG C 56 MET C 59 ARG C 60 GLN C 71 SITE 4 AC3 21 THR C 91 HIS C 92 VAL C 95 GLY C 104 SITE 5 AC3 21 ARG C 131 ASP C 135 ARG C 138 ARG C 140 SITE 6 AC3 21 VAL C 180 SITE 1 AC4 24 PRO G 12 GLY G 13 VAL G 14 GLY G 15 SITE 2 AC4 24 GLY G 16 THR G 17 THR G 18 ASN G 38 SITE 3 AC4 24 PHE G 39 GLY G 40 MET G 43 ARG G 56 SITE 4 AC4 24 ARG G 60 GLN G 71 THR G 91 HIS G 92 SITE 5 AC4 24 GLY G 104 ARG G 131 ARG G 138 ASN G 175 SITE 6 AC4 24 LYS G 176 ASN G 177 GLY G 178 HOH G 199 CRYST1 102.840 102.840 228.720 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 0.009724 0.005614 0.000000 0.00000 SCALE2 0.000000 0.011228 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004372 0.00000