HEADER TRANSFERASE 03-MAY-16 5G3Z TITLE CRYSTAL STRUCTURE OF ADENYLATE KINASE ANCESTOR 3 WITH ZN, MG AND AP5A TITLE 2 BOUND COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADENYLATE KINSE; COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.4.3; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET17B KEYWDS ADENYLATE KINASE, ADP, TRANSFERASE, PHOSPHORYL TRANSFER, NUCLEOTIDE- KEYWDS 2 BINDING EXPDTA X-RAY DIFFRACTION AUTHOR V.NGUYEN,S.KUTTER,J.ENGLISH,D.KERN REVDAT 4 10-JAN-24 5G3Z 1 REMARK LINK REVDAT 3 08-MAY-19 5G3Z 1 REMARK REVDAT 2 01-MAR-17 5G3Z 1 JRNL REVDAT 1 28-DEC-16 5G3Z 0 JRNL AUTH V.NGUYEN,C.WILSON,M.HOEMBERGER,J.B.STILLER,R.V.AGAFONOV, JRNL AUTH 2 S.KUTTER,J.ENGLISH,D.L.THEOBALD,D.KERN JRNL TITL EVOLUTIONARY DRIVERS OF THERMOADAPTATION IN ENZYME JRNL TITL 2 CATALYSIS. JRNL REF SCIENCE V. 355 289 2017 JRNL REFN ESSN 1095-9203 JRNL PMID 28008087 JRNL DOI 10.1126/SCIENCE.AAH3717 REMARK 2 REMARK 2 RESOLUTION. 1.89 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 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) : 1.89 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.50 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 15482 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) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1029 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) : 1.89 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.94 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1122 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.75 REMARK 3 BIN R VALUE (WORKING SET) : 0.3050 REMARK 3 BIN FREE R VALUE SET COUNT : 70 REMARK 3 BIN FREE R VALUE : 0.3080 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1671 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 59 REMARK 3 SOLVENT ATOMS : 118 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.95 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : 0.00000 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): 0.162 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.155 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.113 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.930 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.920 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1755 ; 0.018 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1699 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2371 ; 2.057 ; 2.038 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3931 ; 1.076 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 214 ; 6.065 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 77 ;42.479 ;25.455 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 328 ;15.632 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;13.467 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 262 ; 0.120 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1927 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 357 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 859 ; 1.795 ; 1.845 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 858 ; 1.792 ; 1.840 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1072 ; 2.737 ; 2.749 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 896 ; 3.128 ; 2.191 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 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. REMARK 4 REMARK 4 5G3Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-MAY-16. REMARK 100 THE DEPOSITION ID IS D_1290066711. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-NOV-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00002 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL, SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16553 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.890 REMARK 200 RESOLUTION RANGE LOW (A) : 77.430 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.100 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.18000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.89 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 1.30000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1P3J REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.5 UL OF PROTEIN MIXTURE (20 MG/ML REMARK 280 ADK ANCESTOR 3 AND 10 MM MGAP5A IN 40 MM MOPS PH 7.0, 50 MM NACL, REMARK 280 2 MM TCEP) WAS MIXED WITH 0.5 UL OF MOTHER LIQUOR (1.6 M SODIUM REMARK 280 CITRATE TRIBASIC DEHYDRATE PH 6.5). CRYSTALS WERE GROWN BY REMARK 280 SITTING DROP METHOD AT 18C., VAPOR DIFFUSION, SITTING DROP, REMARK 280 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 33.30850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.71750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.30850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.71750 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 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 LYS A 216 REMARK 465 GLN A 217 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 36 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 88 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG A 88 NE - CZ - NH2 ANGL. DEV. = -4.9 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 ILE A 140 -61.80 -103.18 REMARK 500 ASN A 142 66.75 -158.30 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1216 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 130 SG REMARK 620 2 CYS A 133 SG 120.8 REMARK 620 3 CYS A 150 SG 101.1 105.6 REMARK 620 4 CYS A 153 SG 90.4 123.3 113.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1218 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 AP5 A1217 O2G REMARK 620 2 AP5 A1217 O2D 81.7 REMARK 620 3 HOH A2036 O 85.8 162.1 REMARK 620 4 HOH A2064 O 100.9 95.3 74.4 REMARK 620 5 HOH A2065 O 152.3 125.6 66.5 74.4 REMARK 620 6 HOH A2089 O 88.6 85.3 107.3 170.5 97.5 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1216 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AP5 A 1217 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1218 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5G3Y RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ADENYLATE KINASE ANCESTOR 1 WITH ZN AND ADP REMARK 900 BOUND REMARK 900 RELATED ID: 5G40 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ADENYLATE KINASE ANCESTOR 4 WITH ZN AND AMP- REMARK 900 ADP BOUND REMARK 900 RELATED ID: 5G41 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ADENYLATE KINASE ANCESTOR 4 WITH ZN, MG AND REMARK 900 AP5A BOUND DBREF 5G3Z A 1 217 PDB 5G3Z 5G3Z 1 217 SEQRES 1 A 217 MET ASN LEU VAL LEU MET GLY LEU PRO GLY ALA GLY LYS SEQRES 2 A 217 GLY THR GLN ALA GLU LYS ILE VAL GLU LYS TYR GLY ILE SEQRES 3 A 217 PRO HIS ILE SER THR GLY ASP MET PHE ARG ALA ALA ILE SEQRES 4 A 217 LYS GLU GLY THR GLU LEU GLY LEU LYS ALA LYS SER PHE SEQRES 5 A 217 MET ASP LYS GLY GLU LEU VAL PRO ASP GLU VAL THR ILE SEQRES 6 A 217 GLY ILE VAL ARG GLU ARG LEU SER LYS ASP ASP CYS LYS SEQRES 7 A 217 LYS GLY PHE LEU LEU ASP GLY PHE PRO ARG THR VAL ALA SEQRES 8 A 217 GLN ALA GLU ALA LEU ASP ASN ILE LEU LYS GLU LEU GLY SEQRES 9 A 217 LYS LYS LEU ASP TYR VAL ILE ASN ILE GLU VAL PRO LYS SEQRES 10 A 217 GLU GLU LEU MET GLU ARG LEU THR GLY ARG ARG ILE CYS SEQRES 11 A 217 LYS THR CYS GLY ALA THR TYR HIS LEU ILE PHE ASN PRO SEQRES 12 A 217 PRO LYS VAL GLU GLY VAL CYS ASP LYS CYS GLY GLY GLU SEQRES 13 A 217 LEU TYR GLN ARG ALA ASP ASP ASN GLU GLU THR VAL ALA SEQRES 14 A 217 ASN ARG LEU ASP VAL ASN MET LYS GLN THR GLN PRO LEU SEQRES 15 A 217 LEU ASP PHE TYR GLU GLU LYS GLY TYR LEU ARG ASN ILE SEQRES 16 A 217 ASP GLY GLN GLN ASP ILE ASN LYS VAL PHE ALA ASP ILE SEQRES 17 A 217 ASP ALA LEU LEU GLY GLY LEU LYS GLN HET ZN A1216 1 HET AP5 A1217 57 HET MG A1218 1 HETNAM ZN ZINC ION HETNAM AP5 BIS(ADENOSINE)-5'-PENTAPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 2 ZN ZN 2+ FORMUL 3 AP5 C20 H29 N10 O22 P5 FORMUL 4 MG MG 2+ FORMUL 5 HOH *118(H2 O) HELIX 1 1 GLY A 12 GLY A 25 1 14 HELIX 2 2 THR A 31 GLU A 41 1 11 HELIX 3 3 THR A 43 GLY A 56 1 14 HELIX 4 4 PRO A 60 SER A 73 1 14 HELIX 5 5 LYS A 74 LYS A 78 5 5 HELIX 6 6 THR A 89 LEU A 103 1 15 HELIX 7 7 PRO A 116 GLU A 118 5 3 HELIX 8 8 GLU A 119 GLY A 126 1 8 HELIX 9 9 ARG A 160 ASP A 163 5 4 HELIX 10 10 ASN A 164 GLY A 190 1 27 HELIX 11 11 ASP A 200 GLY A 213 1 14 SHEET 1 AA 5 HIS A 28 SER A 30 0 SHEET 2 AA 5 PHE A 81 ASP A 84 1 O LEU A 82 N ILE A 29 SHEET 3 AA 5 ASN A 2 MET A 6 1 O LEU A 3 N LEU A 83 SHEET 4 AA 5 TYR A 109 GLU A 114 1 O TYR A 109 N VAL A 4 SHEET 5 AA 5 LEU A 192 ASP A 196 1 O ARG A 193 N ASN A 112 SHEET 1 AB 3 THR A 136 HIS A 138 0 SHEET 2 AB 3 ARG A 127 CYS A 130 -1 O ARG A 128 N TYR A 137 SHEET 3 AB 3 LEU A 157 TYR A 158 -1 O TYR A 158 N ILE A 129 LINK SG CYS A 130 ZN ZN A1216 1555 1555 2.23 LINK SG CYS A 133 ZN ZN A1216 1555 1555 2.25 LINK SG CYS A 150 ZN ZN A1216 1555 1555 2.42 LINK SG CYS A 153 ZN ZN A1216 1555 1555 2.43 LINK O2G AP5 A1217 MG MG A1218 1555 1555 2.38 LINK O2D AP5 A1217 MG MG A1218 1555 1555 2.29 LINK MG MG A1218 O HOH A2036 1555 1555 2.66 LINK MG MG A1218 O HOH A2064 1555 1555 2.48 LINK MG MG A1218 O HOH A2065 1555 1555 2.50 LINK MG MG A1218 O HOH A2089 1555 1555 2.61 CISPEP 1 PHE A 86 PRO A 87 0 -13.13 SITE 1 AC1 4 CYS A 130 CYS A 133 CYS A 150 CYS A 153 SITE 1 AC2 40 PRO A 9 GLY A 10 ALA A 11 GLY A 12 SITE 2 AC2 40 LYS A 13 GLY A 14 THR A 15 THR A 31 SITE 3 AC2 40 GLY A 32 ARG A 36 MET A 53 GLU A 57 SITE 4 AC2 40 VAL A 59 THR A 64 GLY A 85 ARG A 88 SITE 5 AC2 40 GLN A 92 ARG A 123 LEU A 124 ARG A 127 SITE 6 AC2 40 THR A 136 TYR A 137 HIS A 138 PHE A 141 SITE 7 AC2 40 ASN A 142 ARG A 160 ARG A 171 GLN A 199 SITE 8 AC2 40 ILE A 201 MG A1218 HOH A2010 HOH A2016 SITE 9 AC2 40 HOH A2017 HOH A2030 HOH A2036 HOH A2042 SITE 10 AC2 40 HOH A2046 HOH A2089 HOH A2100 HOH A2111 SITE 1 AC3 5 AP5 A1217 HOH A2036 HOH A2064 HOH A2065 SITE 2 AC3 5 HOH A2089 CRYST1 66.617 77.435 38.628 90.00 90.00 90.00 P 21 21 2 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 0.015011 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012914 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025888 0.00000