PDB Short entry for 3DAY HEADER LIGASE 30-MAY-08 3DAY TITLE CRYSTAL STRUCTURE OF HUMAN ACYL-COA SYNTHETASE MEDIUM-CHAIN FAMILY TITLE 2 MEMBER 2A (L64P MUTATION) IN COMPLEX WITH AMP-CPP COMPND MOL_ID: 1; COMPND 2 MOLECULE: ACYL-COENZYME A SYNTHETASE ACSM2A, MITOCHONDRIAL PRECURSOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 32-577; COMPND 5 SYNONYM: ACYL-COA SYNTHETASE MEDIUM-CHAIN FAMILY MEMBER 2A, MIDDLE- COMPND 6 CHAIN ACYL-COA SYNTHETASE 2A, BUTYRATE-COA LIGASE 2A, BUTYRYL COMPND 7 COENZYME A SYNTHETASE 2A; COMPND 8 EC: 6.2.1.2; COMPND 9 ENGINEERED: YES; COMPND 10 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 GENE: ACSM2A, ACSM2, MACS2; SOURCE 5 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 6 EXPRESSION_SYSTEM_COMMON: CABBAGE LOOPER; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: HIGH FIVE; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS KEYWDS MIDDLE-CHAIN ACYL-COA SYNTHETASE, XENOBIOTIC/MEDIUM-CHAIN FATTY ACID- KEYWDS 2 COA LIGASE, STRUCTURAL GENOMICS CONSORTIUM, SGC, ATP-BINDING, FATTY KEYWDS 3 ACID METABOLISM, LIPID METABOLISM, MAGNESIUM, METAL-BINDING, KEYWDS 4 MITOCHONDRION, NUCLEOTIDE-BINDING POLYMORPHISM, TRANSIT PEPTIDE, KEYWDS 5 LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR E.S.PILKA,G.T.KOCHAN,W.W.YUE,C.BHATIA,F.VON DELFT,C.H.ARROWSMITH, AUTHOR 2 A.M.EDWARDS,M.WIKSTROM,C.BOUNTRA,U.OPPERMANN,STRUCTURAL GENOMICS AUTHOR 3 CONSORTIUM (SGC) REVDAT 7 30-AUG-23 3DAY 1 REMARK REVDAT 6 20-OCT-21 3DAY 1 REMARK SEQADV LINK REVDAT 5 31-JAN-18 3DAY 1 AUTHOR REVDAT 4 13-JUL-11 3DAY 1 VERSN REVDAT 3 02-FEB-11 3DAY 1 JRNL REVDAT 2 24-FEB-09 3DAY 1 VERSN REVDAT 1 15-JUL-08 3DAY 0 JRNL AUTH G.KOCHAN,E.S.PILKA,F.VON DELFT,U.OPPERMANN,W.W.YUE JRNL TITL STRUCTURAL SNAPSHOTS FOR THE CONFORMATION-DEPENDENT JRNL TITL 2 CATALYSIS BY HUMAN MEDIUM-CHAIN ACYL-COENZYME A SYNTHETASE JRNL TITL 3 ACSM2A. JRNL REF J.MOL.BIOL. V. 388 997 2009 JRNL REFN ISSN 0022-2836 JRNL PMID 19345228 JRNL DOI 10.1016/J.JMB.2009.03.064 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.4.0066 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.51 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 45963 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) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2441 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) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3127 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.15 REMARK 3 BIN R VALUE (WORKING SET) : 0.2190 REMARK 3 BIN FREE R VALUE SET COUNT : 184 REMARK 3 BIN FREE R VALUE : 0.2960 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4150 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 61 REMARK 3 SOLVENT ATOMS : 763 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.97 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.26000 REMARK 3 B22 (A**2) : -0.55000 REMARK 3 B33 (A**2) : 0.81000 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): 0.143 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.146 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.105 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.675 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.925 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4391 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2980 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5986 ; 1.555 ; 1.970 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7308 ; 0.989 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 558 ; 6.312 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 183 ;33.695 ;24.426 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 754 ;13.532 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 23 ;17.191 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 663 ; 0.094 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4849 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 850 ; 0.001 ; 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): 2711 ; 3.048 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1097 ; 1.031 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4395 ; 4.216 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1680 ; 6.747 ; 7.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1580 ; 8.845 ;11.000 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 : 1 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 33 A 569 REMARK 3 ORIGIN FOR THE GROUP (A): 23.9408 -9.3816 -17.9111 REMARK 3 T TENSOR REMARK 3 T11: -0.0389 T22: -0.0360 REMARK 3 T33: -0.0331 T12: 0.0128 REMARK 3 T13: 0.0105 T23: 0.0164 REMARK 3 L TENSOR REMARK 3 L11: 0.3795 L22: 0.4883 REMARK 3 L33: 0.2554 L12: 0.1067 REMARK 3 L13: -0.0029 L23: -0.0580 REMARK 3 S TENSOR REMARK 3 S11: 0.0049 S12: -0.0046 S13: -0.0170 REMARK 3 S21: 0.0050 S22: -0.0106 S23: -0.0366 REMARK 3 S31: -0.0239 S32: -0.0041 S33: 0.0057 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.00 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. ADDITIONAL DENSITY IN THE ACTIVE SITE, PROBABLY REMARK 3 UNIDENTIFIED ENDOGENOUS SUBSTRATE, WAS MODELLED AS A SET OF REMARK 3 UNKNOWN (UNX) ATOMS. REMARK 4 REMARK 4 3DAY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JUN-08. REMARK 100 THE DEPOSITION ID IS D_1000047811. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-MAR-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 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 FR-E SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI REMARK 200 OPTICS : OSMIC REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS HTC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45963 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 32.720 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.08900 REMARK 200 R SYM (I) : 0.05500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.49100 REMARK 200 R SYM FOR SHELL (I) : 0.30300 REMARK 200 <I/SIGMA(I)> 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 REMARK 200 STARTING MODEL: PDB ENTRY 3C5E REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 3350, 0.20M NACL, 0.1M BIS REMARK 280 -TRIS PH 5.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 28.25400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 60.20750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 48.91750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 60.20750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.25400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 48.91750 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 MET A 8 REMARK 465 GLY A 9 REMARK 465 HIS A 10 REMARK 465 HIS A 11 REMARK 465 HIS A 12 REMARK 465 HIS A 13 REMARK 465 HIS A 14 REMARK 465 HIS A 15 REMARK 465 SER A 16 REMARK 465 SER A 17 REMARK 465 GLY A 18 REMARK 465 VAL A 19 REMARK 465 ASP A 20 REMARK 465 LEU A 21 REMARK 465 GLY A 22 REMARK 465 THR A 23 REMARK 465 GLU A 24 REMARK 465 ASN A 25 REMARK 465 LEU A 26 REMARK 465 TYR A 27 REMARK 465 PHE A 28 REMARK 465 GLN A 29 REMARK 465 SER A 30 REMARK 465 MET A 31 REMARK 465 SER A 32 REMARK 465 PRO A 499 REMARK 465 VAL A 500 REMARK 465 MET A 570 REMARK 465 SER A 571 REMARK 465 GLY A 572 REMARK 465 LYS A 573 REMARK 465 ALA A 574 REMARK 465 ARG A 575 REMARK 465 ALA A 576 REMARK 465 GLN A 577 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 62 CE NZ REMARK 470 LYS A 75 CE NZ REMARK 470 LYS A 141 CE NZ REMARK 470 LYS A 196 CD CE NZ REMARK 470 LYS A 377 CE NZ REMARK 470 LYS A 398 CD CE NZ REMARK 470 LYS A 432 CD CE NZ REMARK 470 GLN A 529 CG CD OE1 NE2 REMARK 470 LYS A 566 CE NZ 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 UNK UNX A 681 UNK UNX A 683 1.81 REMARK 500 OE1 GLU A 78 O HOH A 884 1.98 REMARK 500 O HOH A 1115 O HOH A 1316 2.04 REMARK 500 O HOH A 807 O HOH A 1158 2.08 REMARK 500 CD2 HIS A 330 O HOH A 1192 2.09 REMARK 500 O HOH A 746 O HOH A 1389 2.12 REMARK 500 CD2 LEU A 368 CE MET A 371 2.12 REMARK 500 UNK UNX A 690 UNK UNX A 691 2.18 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 OD2 ASP A 189 O HOH A 1109 4445 1.85 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 TRP A 35 55.34 -145.94 REMARK 500 VAL A 50 -59.73 -123.84 REMARK 500 LEU A 238 -63.44 -96.29 REMARK 500 LEU A 273 -63.94 -106.27 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 MG A 601 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MET A 483 O REMARK 620 2 HIS A 485 O 89.8 REMARK 620 3 VAL A 488 O 110.9 99.1 REMARK 620 4 HOH A 924 O 78.2 160.2 71.3 REMARK 620 5 HOH A 936 O 75.4 90.2 168.6 101.7 REMARK 620 6 HOH A 939 O 167.0 101.9 73.1 92.0 98.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 602 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 APC A 606 O1G REMARK 620 2 APC A 606 O1B 86.2 REMARK 620 3 HOH A 791 O 100.3 92.8 REMARK 620 4 HOH A1361 O 167.0 85.2 89.9 REMARK 620 5 HOH A1362 O 92.8 178.6 86.5 95.9 REMARK 620 6 HOH A1411 O 85.9 90.7 173.1 84.5 90.2 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 MG A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE APC A 606 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS A 607 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 608 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3B7W RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN ACYL-COA SYNTHETASE MEDIUM-CHAIN FAMILY REMARK 900 MEMBER 2A (L64P MUTANT) REMARK 900 RELATED ID: 3C5E RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN ACYL-COA SYNTHETASE MEDIUM-CHAIN FAMILY REMARK 900 MEMBER 2A (L64P MUTANT) IN COMPLEX WITH ATP DBREF 3DAY A 32 577 UNP Q08AH3 ACS2A_HUMAN 32 577 SEQADV 3DAY MET A 8 UNP Q08AH3 EXPRESSION TAG SEQADV 3DAY GLY A 9 UNP Q08AH3 EXPRESSION TAG SEQADV 3DAY HIS A 10 UNP Q08AH3 EXPRESSION TAG SEQADV 3DAY HIS A 11 UNP Q08AH3 EXPRESSION TAG SEQADV 3DAY HIS A 12 UNP Q08AH3 EXPRESSION TAG SEQADV 3DAY HIS A 13 UNP Q08AH3 EXPRESSION TAG SEQADV 3DAY HIS A 14 UNP Q08AH3 EXPRESSION TAG SEQADV 3DAY HIS A 15 UNP Q08AH3 EXPRESSION TAG SEQADV 3DAY SER A 16 UNP Q08AH3 EXPRESSION TAG SEQADV 3DAY SER A 17 UNP Q08AH3 EXPRESSION TAG SEQADV 3DAY GLY A 18 UNP Q08AH3 EXPRESSION TAG SEQADV 3DAY VAL A 19 UNP Q08AH3 EXPRESSION TAG SEQADV 3DAY ASP A 20 UNP Q08AH3 EXPRESSION TAG SEQADV 3DAY LEU A 21 UNP Q08AH3 EXPRESSION TAG SEQADV 3DAY GLY A 22 UNP Q08AH3 EXPRESSION TAG SEQADV 3DAY THR A 23 UNP Q08AH3 EXPRESSION TAG SEQADV 3DAY GLU A 24 UNP Q08AH3 EXPRESSION TAG SEQADV 3DAY ASN A 25 UNP Q08AH3 EXPRESSION TAG SEQADV 3DAY LEU A 26 UNP Q08AH3 EXPRESSION TAG SEQADV 3DAY TYR A 27 UNP Q08AH3 EXPRESSION TAG SEQADV 3DAY PHE A 28 UNP Q08AH3 EXPRESSION TAG SEQADV 3DAY GLN A 29 UNP Q08AH3 EXPRESSION TAG SEQADV 3DAY SER A 30 UNP Q08AH3 EXPRESSION TAG SEQADV 3DAY MET A 31 UNP Q08AH3 EXPRESSION TAG SEQADV 3DAY PRO A 64 UNP Q08AH3 LEU 64 ENGINEERED MUTATION SEQRES 1 A 570 MET GLY HIS HIS HIS HIS HIS HIS SER SER GLY VAL ASP SEQRES 2 A 570 LEU GLY THR GLU ASN LEU TYR PHE GLN SER MET SER LEU SEQRES 3 A 570 GLN TRP GLY HIS GLN GLU VAL PRO ALA LYS PHE ASN PHE SEQRES 4 A 570 ALA SER ASP VAL LEU ASP HIS TRP ALA ASP MET GLU LYS SEQRES 5 A 570 ALA GLY LYS ARG PRO PRO SER PRO ALA LEU TRP TRP VAL SEQRES 6 A 570 ASN GLY LYS GLY LYS GLU LEU MET TRP ASN PHE ARG GLU SEQRES 7 A 570 LEU SER GLU ASN SER GLN GLN ALA ALA ASN VAL LEU SER SEQRES 8 A 570 GLY ALA CYS GLY LEU GLN ARG GLY ASP ARG VAL ALA VAL SEQRES 9 A 570 VAL LEU PRO ARG VAL PRO GLU TRP TRP LEU VAL ILE LEU SEQRES 10 A 570 GLY CYS ILE ARG ALA GLY LEU ILE PHE MET PRO GLY THR SEQRES 11 A 570 ILE GLN MET LYS SER THR ASP ILE LEU TYR ARG LEU GLN SEQRES 12 A 570 MET SER LYS ALA LYS ALA ILE VAL ALA GLY ASP GLU VAL SEQRES 13 A 570 ILE GLN GLU VAL ASP THR VAL ALA SER GLU CYS PRO SER SEQRES 14 A 570 LEU ARG ILE LYS LEU LEU VAL SER GLU LYS SER CYS ASP SEQRES 15 A 570 GLY TRP LEU ASN PHE LYS LYS LEU LEU ASN GLU ALA SER SEQRES 16 A 570 THR THR HIS HIS CYS VAL GLU THR GLY SER GLN GLU ALA SEQRES 17 A 570 SER ALA ILE TYR PHE THR SER GLY THR SER GLY LEU PRO SEQRES 18 A 570 LYS MET ALA GLU HIS SER TYR SER SER LEU GLY LEU LYS SEQRES 19 A 570 ALA LYS MET ASP ALA GLY TRP THR GLY LEU GLN ALA SER SEQRES 20 A 570 ASP ILE MET TRP THR ILE SER ASP THR GLY TRP ILE LEU SEQRES 21 A 570 ASN ILE LEU CYS SER LEU MET GLU PRO TRP ALA LEU GLY SEQRES 22 A 570 ALA CYS THR PHE VAL HIS LEU LEU PRO LYS PHE ASP PRO SEQRES 23 A 570 LEU VAL ILE LEU LYS THR LEU SER SER TYR PRO ILE LYS SEQRES 24 A 570 SER MET MET GLY ALA PRO ILE VAL TYR ARG MET LEU LEU SEQRES 25 A 570 GLN GLN ASP LEU SER SER TYR LYS PHE PRO HIS LEU GLN SEQRES 26 A 570 ASN CYS VAL THR VAL GLY GLU SER LEU LEU PRO GLU THR SEQRES 27 A 570 LEU GLU ASN TRP ARG ALA GLN THR GLY LEU ASP ILE ARG SEQRES 28 A 570 GLU SER TYR GLY GLN THR GLU THR GLY LEU THR CYS MET SEQRES 29 A 570 VAL SER LYS THR MET LYS ILE LYS PRO GLY TYR MET GLY SEQRES 30 A 570 THR ALA ALA SER CYS TYR ASP VAL GLN ILE ILE ASP ASP SEQRES 31 A 570 LYS GLY ASN VAL LEU PRO PRO GLY THR GLU GLY ASP ILE SEQRES 32 A 570 GLY ILE ARG VAL LYS PRO ILE ARG PRO ILE GLY ILE PHE SEQRES 33 A 570 SER GLY TYR VAL ASP ASN PRO ASP LYS THR ALA ALA ASN SEQRES 34 A 570 ILE ARG GLY ASP PHE TRP LEU LEU GLY ASP ARG GLY ILE SEQRES 35 A 570 LYS ASP GLU ASP GLY TYR PHE GLN PHE MET GLY ARG ALA SEQRES 36 A 570 ASP ASP ILE ILE ASN SER SER GLY TYR ARG ILE GLY PRO SEQRES 37 A 570 SER GLU VAL GLU ASN ALA LEU MET GLU HIS PRO ALA VAL SEQRES 38 A 570 VAL GLU THR ALA VAL ILE SER SER PRO ASP PRO VAL ARG SEQRES 39 A 570 GLY GLU VAL VAL LYS ALA PHE VAL VAL LEU ALA SER GLN SEQRES 40 A 570 PHE LEU SER HIS ASP PRO GLU GLN LEU THR LYS GLU LEU SEQRES 41 A 570 GLN GLN HIS VAL LYS SER VAL THR ALA PRO TYR LYS TYR SEQRES 42 A 570 PRO ARG LYS ILE GLU PHE VAL LEU ASN LEU PRO LYS THR SEQRES 43 A 570 VAL THR GLY LYS ILE GLN ARG ALA LYS LEU ARG ASP LYS SEQRES 44 A 570 GLU TRP LYS MET SER GLY LYS ALA ARG ALA GLN HET MG A 601 1 HET MG A 602 1 HET CL A 603 1 HET CL A 604 1 HET CL A 605 1 HET APC A 606 31 HET TRS A 607 8 HET UNX A 681 1 HET UNX A 682 1 HET UNX A 683 1 HET UNX A 684 1 HET UNX A 685 1 HET UNX A 686 1 HET UNX A 687 1 HET UNX A 688 1 HET UNX A 689 1 HET UNX A 690 1 HET UNX A 691 1 HET GOL A 608 6 HETNAM MG MAGNESIUM ION HETNAM CL CHLORIDE ION HETNAM APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETNAM UNX UNKNOWN ATOM OR ION HETNAM GOL GLYCEROL HETSYN APC ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE HETSYN TRS TRIS BUFFER HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 MG 2(MG 2+) FORMUL 4 CL 3(CL 1-) FORMUL 7 APC C11 H18 N5 O12 P3 FORMUL 8 TRS C4 H12 N O3 1+ FORMUL 9 UNX 11(X) FORMUL 20 GOL C3 H8 O3 FORMUL 21 HOH *763(H2 O) HELIX 1 1 ASN A 45 VAL A 50 1 6 HELIX 2 2 VAL A 50 ALA A 60 1 11 HELIX 3 3 PHE A 83 GLY A 99 1 17 HELIX 4 4 VAL A 116 GLY A 130 1 15 HELIX 5 5 LYS A 141 LYS A 153 1 13 HELIX 6 6 VAL A 163 ALA A 171 1 9 HELIX 7 7 SER A 172 CYS A 174 5 3 HELIX 8 8 PHE A 194 ALA A 201 1 8 HELIX 9 9 TYR A 235 ALA A 246 1 12 HELIX 10 10 TRP A 265 SER A 272 1 8 HELIX 11 11 LEU A 273 GLY A 280 1 8 HELIX 12 12 ASP A 292 TYR A 303 1 12 HELIX 13 13 ALA A 311 GLN A 320 1 10 HELIX 14 14 LEU A 342 GLY A 354 1 13 HELIX 15 15 ASN A 429 ASN A 436 1 8 HELIX 16 16 ASP A 463 ILE A 465 5 3 HELIX 17 17 GLY A 474 GLU A 484 1 11 HELIX 18 18 SER A 513 LEU A 516 5 4 HELIX 19 19 ASP A 519 THR A 535 1 17 HELIX 20 20 ALA A 536 TYR A 540 5 5 HELIX 21 21 GLN A 559 LYS A 569 1 11 SHEET 1 A 9 GLU A 78 ASN A 82 0 SHEET 2 A 9 PRO A 67 VAL A 72 -1 N ALA A 68 O TRP A 81 SHEET 3 A 9 CYS A 282 HIS A 286 1 O THR A 283 N TRP A 70 SHEET 4 A 9 ILE A 256 THR A 259 1 N MET A 257 O PHE A 284 SHEET 5 A 9 SER A 307 MET A 309 1 O SER A 307 N TRP A 258 SHEET 6 A 9 ASN A 333 THR A 336 1 O VAL A 335 N MET A 308 SHEET 7 A 9 ARG A 358 GLN A 363 1 O ARG A 358 N CYS A 334 SHEET 8 A 9 GLY A 367 MET A 371 -1 O CYS A 370 N TYR A 361 SHEET 9 A 9 THR A 385 ALA A 386 -1 O THR A 385 N MET A 371 SHEET 1 B 5 ILE A 132 PRO A 135 0 SHEET 2 B 5 ARG A 108 VAL A 112 1 N VAL A 109 O ILE A 132 SHEET 3 B 5 ALA A 156 GLY A 160 1 O VAL A 158 N VAL A 112 SHEET 4 B 5 ILE A 179 VAL A 183 1 O LEU A 181 N ILE A 157 SHEET 5 B 5 LEU A 192 ASN A 193 1 O LEU A 192 N LYS A 180 SHEET 1 C 3 ALA A 215 PHE A 220 0 SHEET 2 C 3 MET A 230 SER A 234 -1 O HIS A 233 N SER A 216 SHEET 3 C 3 GLY A 425 TYR A 426 -1 O GLY A 425 N GLU A 232 SHEET 1 D 4 VAL A 392 ILE A 395 0 SHEET 2 D 4 GLY A 408 ARG A 413 -1 O ASP A 409 N ILE A 395 SHEET 3 D 4 PHE A 441 LYS A 450 -1 O ASP A 446 N ILE A 410 SHEET 4 D 4 ILE A 437 ARG A 438 -1 N ARG A 438 O PHE A 441 SHEET 1 E 4 VAL A 392 ILE A 395 0 SHEET 2 E 4 GLY A 408 ARG A 413 -1 O ASP A 409 N ILE A 395 SHEET 3 E 4 PHE A 441 LYS A 450 -1 O ASP A 446 N ILE A 410 SHEET 4 E 4 PHE A 456 ARG A 461 -1 O MET A 459 N ARG A 447 SHEET 1 F 2 ILE A 466 SER A 468 0 SHEET 2 F 2 TYR A 471 ILE A 473 -1 O ILE A 473 N ILE A 466 SHEET 1 G 3 VAL A 488 PRO A 497 0 SHEET 2 G 3 GLU A 503 LEU A 511 -1 O VAL A 510 N GLU A 490 SHEET 3 G 3 LYS A 543 VAL A 547 1 O GLU A 545 N ALA A 507 LINK O MET A 483 MG MG A 601 1555 1555 2.62 LINK O HIS A 485 MG MG A 601 1555 1555 2.38 LINK O VAL A 488 MG MG A 601 1555 1555 2.57 LINK MG MG A 601 O HOH A 924 1555 1555 2.27 LINK MG MG A 601 O HOH A 936 1555 1555 2.73 LINK MG MG A 601 O HOH A 939 1555 1555 2.79 LINK MG MG A 602 O1G APC A 606 1555 1555 2.11 LINK MG MG A 602 O1B APC A 606 1555 1555 2.09 LINK MG MG A 602 O HOH A 791 1555 1555 2.08 LINK MG MG A 602 O HOH A1361 1555 1555 2.26 LINK MG MG A 602 O HOH A1362 1555 1555 2.16 LINK MG MG A 602 O HOH A1411 1555 1555 2.24 CISPEP 1 LYS A 415 PRO A 416 0 3.06 SITE 1 AC1 5 MET A 483 HIS A 485 HOH A 924 HOH A 936 SITE 2 AC1 5 HOH A 939 SITE 1 AC2 4 HOH A 791 HOH A1361 HOH A1362 HOH A1411 SITE 1 AC3 3 ARG A 316 LEU A 342 THR A 345 SITE 1 AC4 6 LEU A 288 PRO A 289 LYS A 290 PHE A 291 SITE 2 AC4 6 ASP A 292 HOH A 694 SITE 1 AC5 2 ASP A 49 HIS A 53 SITE 1 AC6 29 THR A 221 SER A 222 GLY A 223 THR A 224 SITE 2 AC6 29 SER A 225 LYS A 229 GLY A 338 GLU A 339 SITE 3 AC6 29 SER A 340 GLU A 359 SER A 360 TYR A 361 SITE 4 AC6 29 GLY A 362 GLN A 363 THR A 364 ASP A 446 SITE 5 AC6 29 PHE A 458 ARG A 461 LYS A 557 HOH A 734 SITE 6 AC6 29 HOH A 761 HOH A 776 HOH A 791 HOH A 874 SITE 7 AC6 29 HOH A1211 HOH A1361 HOH A1362 HOH A1402 SITE 8 AC6 29 HOH A1411 SITE 1 AC7 4 MET A 80 TRP A 81 GLU A 85 HOH A 910 SITE 1 AC8 8 TRP A 71 LYS A 77 LEU A 79 PRO A 117 SITE 2 AC8 8 GLU A 118 LYS A 195 HOH A 832 HOH A 883 CRYST1 56.508 97.835 120.415 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 0.017697 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010221 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008305 0.00000