HEADER TRANSFERASE 12-APR-13 4K46 TITLE CRYSTAL STRUCTURE OF ADENYLATE KINASE FROM PHOTOBACTERIUM PROFUNDUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADENYLATE KINASE; COMPND 3 CHAIN: A; 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: PHOTOBACTERIUM PROFUNDUM; SOURCE 3 ORGANISM_TAXID: 74109; SOURCE 4 GENE: ADK, PBPRA1024; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSFERASE, PHOSPHORYL TRANSFER REACTION, CONFORMATIONAL CHANGES, KEYWDS 2 PRESSURE-DEPENDENT ACTIVITY INCREASE, PHOSPHORYL GRANSFER REACTION, KEYWDS 3 CONFORMATIONAL CHANGES OF LIDS DOMAINS, ATP BINDING, AMP BINDING, KEYWDS 4 ADP BINDING, PHOSPHORYL TRANSFER EXPDTA X-RAY DIFFRACTION AUTHOR Y.-J.CHO,S.J.KERNS,D.KERN REVDAT 2 28-FEB-24 4K46 1 REMARK REVDAT 1 16-JUL-14 4K46 0 JRNL AUTH Y.-J.CHO,S.J.KERNS,D.KERN JRNL TITL ALIKE BUT DIFFERENT: ADENYLATE KINASES FROM E. COLI, JRNL TITL 2 AQUIFEX, AND P. PROFUNDUM JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.01 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7.2_865 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.01 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.16 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 14833 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 753 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 50.1805 - 3.4368 1.00 2999 128 0.1578 0.1871 REMARK 3 2 3.4368 - 2.7279 1.00 2819 155 0.1771 0.2454 REMARK 3 3 2.7279 - 2.3831 1.00 2759 170 0.1763 0.2410 REMARK 3 4 2.3831 - 2.1652 0.99 2773 134 0.1643 0.2164 REMARK 3 5 2.1652 - 2.0100 1.00 2730 166 0.1684 0.2392 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.90 REMARK 3 SHRINKAGE RADIUS : 0.60 REMARK 3 K_SOL : 0.40 REMARK 3 B_SOL : 39.52 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.720 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.72 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.44100 REMARK 3 B22 (A**2) : -3.62680 REMARK 3 B33 (A**2) : 4.06780 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: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 1746 REMARK 3 ANGLE : 1.208 2375 REMARK 3 CHIRALITY : 0.074 269 REMARK 3 PLANARITY : 0.004 304 REMARK 3 DIHEDRAL : 17.640 654 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 4K46 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-MAY-13. REMARK 100 THE DEPOSITION ID IS D_1000078868. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979306 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14921 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.010 REMARK 200 RESOLUTION RANGE LOW (A) : 50.160 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.07400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.01 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 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 : 0.078 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.3M AMMONIUM SULFATE, 100MM REMARK 280 IMIDAZOLE, PH 7.9, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 291K 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 21.29500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.84000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.11500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.84000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.29500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.11500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 O HOH A 568 O HOH A 582 2.08 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 A 585 O HOH A 586 2454 1.93 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 138 65.80 -166.89 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 ADP A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AMP A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 303 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4JZK RELATED DB: PDB REMARK 900 VERY HOMOLOGOUS PROTEINS BUT DIFFERENT SPECIES (E. COLI VS. P. REMARK 900 PROFUNDUM) ADKS DBREF 4K46 A 1 214 UNP Q6LTE1 KAD_PHOPR 1 214 SEQRES 1 A 214 MET ARG ILE ILE LEU LEU GLY ALA PRO GLY ALA GLY LYS SEQRES 2 A 214 GLY THR GLN ALA GLN PHE ILE MET ALA LYS PHE GLY ILE SEQRES 3 A 214 PRO GLN ILE SER THR GLY ASP MET LEU ARG ALA ALA ILE SEQRES 4 A 214 LYS ALA GLY THR GLU LEU GLY LYS GLN ALA LYS SER VAL SEQRES 5 A 214 ILE ASP ALA GLY GLN LEU VAL SER ASP ASP ILE ILE LEU SEQRES 6 A 214 GLY LEU VAL LYS GLU ARG ILE ALA GLN ASP ASP CYS ALA SEQRES 7 A 214 LYS GLY PHE LEU LEU ASP GLY PHE PRO ARG THR ILE PRO SEQRES 8 A 214 GLN ALA ASP GLY LEU LYS GLU VAL GLY VAL VAL VAL ASP SEQRES 9 A 214 TYR VAL ILE GLU PHE ASP VAL ALA ASP SER VAL ILE VAL SEQRES 10 A 214 GLU ARG MET ALA GLY ARG ARG ALA HIS LEU ALA SER GLY SEQRES 11 A 214 ARG THR TYR HIS ASN VAL TYR ASN PRO PRO LYS VAL GLU SEQRES 12 A 214 GLY LYS ASP ASP VAL THR GLY GLU ASP LEU VAL ILE ARG SEQRES 13 A 214 GLU ASP ASP LYS GLU GLU THR VAL LEU ALA ARG LEU GLY SEQRES 14 A 214 VAL TYR HIS ASN GLN THR ALA PRO LEU ILE ALA TYR TYR SEQRES 15 A 214 GLY LYS GLU ALA GLU ALA GLY ASN THR GLN TYR LEU LYS SEQRES 16 A 214 PHE ASP GLY THR LYS ALA VAL ALA GLU VAL SER ALA GLU SEQRES 17 A 214 LEU GLU LYS ALA LEU ALA HET ADP A 301 27 HET AMP A 302 23 HET PO4 A 303 5 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM AMP ADENOSINE MONOPHOSPHATE HETNAM PO4 PHOSPHATE ION FORMUL 2 ADP C10 H15 N5 O10 P2 FORMUL 3 AMP C10 H14 N5 O7 P FORMUL 4 PO4 O4 P 3- FORMUL 5 HOH *199(H2 O) HELIX 1 1 GLY A 12 GLY A 25 1 14 HELIX 2 2 THR A 31 GLY A 42 1 12 HELIX 3 3 THR A 43 GLY A 56 1 14 HELIX 4 4 SER A 60 ALA A 73 1 14 HELIX 5 5 GLN A 74 ALA A 78 5 5 HELIX 6 6 THR A 89 VAL A 99 1 11 HELIX 7 7 ALA A 112 ALA A 121 1 10 HELIX 8 8 ARG A 156 ASP A 159 5 4 HELIX 9 9 LYS A 160 THR A 175 1 16 HELIX 10 10 ALA A 176 ALA A 188 1 13 HELIX 11 11 ALA A 201 LEU A 213 1 13 SHEET 1 A 5 GLN A 28 SER A 30 0 SHEET 2 A 5 PHE A 81 ASP A 84 1 O LEU A 82 N ILE A 29 SHEET 3 A 5 ARG A 2 LEU A 6 1 N ILE A 3 O LEU A 83 SHEET 4 A 5 TYR A 105 ASP A 110 1 O ILE A 107 N ILE A 4 SHEET 5 A 5 GLN A 192 ASP A 197 1 O LEU A 194 N GLU A 108 SHEET 1 B 2 ARG A 123 HIS A 126 0 SHEET 2 B 2 ARG A 131 HIS A 134 -1 O TYR A 133 N ARG A 124 CISPEP 1 PHE A 86 PRO A 87 0 -3.12 SITE 1 AC1 22 GLY A 10 ALA A 11 GLY A 12 LYS A 13 SITE 2 AC1 22 GLY A 14 THR A 15 ARG A 119 MET A 120 SITE 3 AC1 22 ARG A 123 THR A 132 TYR A 133 HIS A 134 SITE 4 AC1 22 TYR A 137 GLY A 198 LYS A 200 VAL A 202 SITE 5 AC1 22 HOH A 402 HOH A 406 HOH A 418 HOH A 427 SITE 6 AC1 22 HOH A 431 HOH A 446 SITE 1 AC2 20 THR A 31 GLY A 32 LEU A 35 ARG A 36 SITE 2 AC2 20 ILE A 53 GLN A 57 VAL A 59 ILE A 64 SITE 3 AC2 20 GLY A 85 ARG A 88 GLN A 92 ARG A 156 SITE 4 AC2 20 ARG A 167 HOH A 409 HOH A 410 HOH A 431 SITE 5 AC2 20 HOH A 433 HOH A 457 HOH A 558 HOH A 597 SITE 1 AC3 2 MET A 1 HOH A 561 CRYST1 42.590 70.230 71.680 90.00 90.00 90.00 P 21 21 21 4 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 0.023480 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014239 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013951 0.00000